145 questions
-1
votes
0
answers
17
views
How can I install angsd on a linux platform? [closed]
I'm trying to install angsd for running paired-end screening data analysis and after git clone and going into the folder, when running the command make, I keep getting the following error:
kprobaln.c:(...
- 1
1
vote
1
answer
141
views
BLAST+ blastn fmt output 17 (sam) incorrect formatting
I am using BLAST+ to map some nanopore reads onto my own reference. I am using multiple output file formats, mostly 0 (blast-style visual alignment) and 6 (the tsv file) without issue. All the ...
- 31
0
votes
1
answer
76
views
Find out of sequence data in a column of text
I have a table in SQL Server that tracks the working status changes of sales orders.
When the order is first entered it is automatically in a status of NEW.
When the order is populated with product ...
- 35
0
votes
1
answer
70
views
How to evaluate SCORM rule conditions against objective tracking model and CMI data?
I’m working on a SCORM package where I'm evaluating rule conditions defined in the sequencing rules against objectives before delivering an activity. I understand that the ...
0
votes
1
answer
164
views
My LSTM model returns empty with no output and no parameters captured
I am building an LSTM model for sentiment analysis using a hotel review dataset. However, the model always returns empty with empty output and parameters each time I run the code.
I have followed many ...
- 19
0
votes
0
answers
195
views
Graphics not appearing at the correct time in CodeHS
I am doing a project for school on CodeHS using Javascript. It is a game in which the user tries to move a character across the screen by pressing numbers to indicate which direction they want it to ...
- 51
0
votes
0
answers
67
views
How to plot a table reflecting gene sequencing data qualitatively
I'm looking for ways to plot sequencing data like this:
It seems to be a common plot. I know there are ways to plot a table filled with colors from a relevant post
tableplot <- function(ret, nrow, ...
- 11
0
votes
0
answers
68
views
How to record an audio sequence to a file in Node.js?
I've made a Node.js program for generating procedural animations from a simulation. I want to add sound effects to the animations, but I haven't been able to find any libraries for generating a ...
0
votes
0
answers
174
views
Create sequence number based on multiple columns
I have an excel spreadsheet where I have
City PN No Accepted Date
bracknell Each PN is unique i.e BRK-1-PN222 26/7/23
Ipswich ...
1
vote
0
answers
74
views
Longstitch error make: command: Command not found *** No rule to make target
I installed Longstitch and ran the test script with no issues. The output files matched the expected output files. But when I am now trying to run Longstitch on my own data I am getting this error.
(...
- 41
0
votes
0
answers
66
views
Optimise waypoints to reach the destination
We are facing problem in sequencing geocodes to reach destination(Single destination for all pickup) with minimum cost.
Lets assume we have a Set of n geocodes as a pick up locations and a destination ...
0
votes
0
answers
160
views
"no such file or directory" - but lists a file location that has not been specified
I am running QC for bulk RNAseq and ran the following code:
base_dir <- "/data/dpag-paupar-kap1/mert4522/FASTQ/0.2Data2"
fastqc_dir <- "/data/dpag-paupar-kap1/mert4522/FASTQ/0....
0
votes
2
answers
525
views
Missing Aligned.sortedbyCoord.out.bam file after using STAR
I am new to RNA-Sequencing and I am having trouble with my alignment. I am using STAR and I seem to be missing one of the output files I believe I need for the next step. I can not find my Aligned....
- 1
-1
votes
1
answer
170
views
Visualizing 3 features simultaneously in Seurat/single cell RNA sequencing
I am wondering if it is possible to visualize 3 features from a single cell RNA sequencing data set simultaneously.
I use the blend function of DimPlot to visualize 2 features, but is it possible to ...
- 3
-1
votes
1
answer
60
views
Data/matrix manipulation in R [duplicate]
Dear stackoverflow community,
I think im experienced with R, but last week R proved me wrong.
I think my problem is very easy to solve, but i can't, so im reaching out for you guys!
I got a problem ...
- 11
1
vote
1
answer
190
views
Missing Output Exception Error in Snakemake
I am using snakemake version 7.30.1
I am trying to run my snakemake workflow using snakemake --cores 4. Snakemake seems to be able to locate the input files and seems to start to complete the steps of ...
- 11
0
votes
1
answer
137
views
Convert a 'DeseqStats' object into a pandas dataframe?
Is it possible to convert a DeseqStats object from PyDESeq2 into a Pandas DataFrame?
results_summary = stat_res results_as_html = results_summary.tables[1].as_html() pd.read_html(results_as_html, ...
- 11
1
vote
0
answers
432
views
Samtools mpileup : error reading from input file
I am writing a code to analyse yeast sequencing data using R. I was able to do the alignment using BWA and thus obtain a .bam file and its .bai index using samtools. My next step is to perform variant ...
- 11
0
votes
1
answer
60
views
Sorting data by time interval using start and end times in R
I have a couple of data collected by date and time. The collected data is by time interval. I'm doing gas analysis by sensor. So the sensor gave me data in the following form
RFID `Farm Name` `Start ...
0
votes
1
answer
933
views
How to sequence datalayer.push?
I have a question regarding GA4 Enhanced Ecommerce Tracking with GTM - although the problem isn't specific to GA4 or Ecommerce Tracking.
The Situation
the shop does use usercentrics as cookie ...
0
votes
1
answer
889
views
How can I convert a fsa_nt file to FASTA?
Im trying to convert a file downloaded from NCBI containing contigs of a bacterial genome. For further analysis I need to have it in FASta format.
I tried converting via seqkit, but it does not work.
0
votes
1
answer
93
views
What is the idiomatic way to combine member function calls with other function calls in Scala? [duplicate]
Say we have an object (e.g. a list) in Scala, and we want to sequence user-defined functions with object member functions, for instance:
g(l.map(f)
.foldRight(...))
.map(h)
If the sequence of ...
- 152
0
votes
0
answers
87
views
Having some problem with filtering data for single cell RNA sequencing
Currently I am trying to filter some data for single cell RNA sequencing, and this process requires the use of python. I am trying to run the following codes and I am facing some errors.
%pylab inline
...
- 21
1
vote
1
answer
227
views
Suggestions on Analyzing Protein Sequences Similarity
I want to write code to analyze short protein sequences and determine their similarity. I have no reference sequence but rather I want to write some sort of for loop to compare them all to each other ...
- 11
3
votes
0
answers
279
views
Trimmomatic-0.39 error message "Unknown option -baseout ..."
I have used Trimmomatic-0.39 few times already for trimming some sequencing data. This time I tried the option -baseout as stated in the manual but it does not recognise it as a valid option and the ...
- 31
0
votes
0
answers
50
views
Omitting NAs from Data
First time posting. Apologies if I'm not as clear as I intend.
I have an excel (xlxs) spreadsheet of data; it's sequencing data if that helps. Generally indexed as follows:
column 1 = organism ...
0
votes
0
answers
260
views
Efficient algorithm for job sequencing, but with variable times needed
Problem: Given N tasks with potentially non-unique deadlines d1,...,dN and time needed t1,...,tN to complete each one (in hours), output a schedule that maximizes the number of deadlines met. Only 1 ...
- 35
1
vote
0
answers
57
views
Segmentation fault on an old software loading fasta?
I'm fairly new to c++ but I'm trying to learn. I've been tasked with implementing an old software called snpomatic in our pipelines.
I could successfully build the program and run it with some ...
- 11
1
vote
1
answer
5k
views
Pheatmap Annotation Row
Excuse Essay
So I’ve done a Deseq analysis, then taken the counts file, applied the same names and then removed an NA values , then created a ?tibble/table called sigs, which I then turn into a Data ...
- 43
1
vote
1
answer
262
views
Find sequencing reads with insertions longer than number
I'm trying to isolate, from a bam file, those sequencing reads that have insertions longer than number (let's say 50bp). I guess I can do that using the cigar but I don't know any easy way to parse it ...
- 67
0
votes
1
answer
2k
views
How to generate a custom bed file to use for bedtools intersect?
I have a custom reference genome, gene.fa and 18 bed files. I want to generate a bed file that contains a region of interest, 5100-5600 bp, as a single entry that I can use for intersection using ...
- 121
0
votes
1
answer
226
views
Interpolate and insert missing rows into dataframe R
I am working with a large time series of oceanographic data which needs a lot of manipulation.
I have several days of data missing and would like to interpolate them. Specifically date/depth/...
- 91
-1
votes
1
answer
1k
views
As I run the Cellranger count, I get the following error: "The argument '--fastqs <PATH>...' requires a value but none was supplied"
I am following the 10x Cellranger steps and using the same files for cellranger count. I run this from the fastq directory that contains all the PBMCs fastq files and the GRCh38 files too.
0
votes
0
answers
325
views
Task sequencing based on dependent tasks with parallel execution
Having a scenario where I need to identify task sequence and execute tasks possible indenpendent flows/tasks parallely. for example
Task 1
Task 2 ->Task 11 and task-3
Task 3 -> Task 1
Task 4 -&...
0
votes
2
answers
3k
views
How can I convert Affymetrix probes into gene Symbols?
I have carried out Affymetrix data analysis with oligo and limma. Now I need to perform the gene enrichment analysis on the upregulated and downregulated genes (on EnrichR, by searching the gene ...
4
votes
3
answers
258
views
Haskell >> operator with two lists
For a college assignment I am learning Haskell and when reading about the do-notation and sequencing with >>= and >> I came across this behaviour that I did not expect.
[1,2,3] >> [1]...
0
votes
1
answer
82
views
Binary search between two files in C
I'm trying to apply some previously written code to some DNA sequencing data that I have collected. I would like to match my sequencing reads to a document containing specific barcodes and output the ...
1
vote
2
answers
118
views
Why might the Scheme `filter` form not process list elements 'in order'?
(filter procedure list) applies procedure to each element of list
and returns a new list containing only the elements for which procedure
returns true.
(R. Kent Dybvig The Scheme Programming Language)
...
- 820
2
votes
1
answer
837
views
How do I run this Bismark Bisulfite Sequencing program?
I am very new to coding so I'm not really sure how to approach this. I wanted to look at some data that we got and sequence them using Bismark. I already used Trim Galore to pare the reads, now I ...
- 23
0
votes
1
answer
197
views
STAR mapping is creating empty BAM file
I'm trying to run STAR but I am getting an empty BAM file. Does anyone know why this is happening and how to fix it?
iCount mapstar demultiplexed/demux_NNNGGCGNN.fastq.gz hs88 mapping_NNNGGCGNN \
> ...
- 15
1
vote
1
answer
925
views
set a sequence on a list of items
I need to set up a recursive function in C# to set the sequence number of a list of items. More specifically a bom. For each bom level, I need to start the sequence at 10, and increment of 10. How ...
- 11
1
vote
0
answers
35
views
Can analysis of GWAS/WES/WGS be performed with DNA from saliva in combination with DNA from blood?
Can statistical analyses (GWAS/WES/WGS) be performed with DNA from saliva in combination with DNA from blood? Is there a chance of bias? First, I think DNA=DNA, in other words, no matter how the 'DNA ...
1
vote
2
answers
435
views
haskell *> sequencing operator
I have a question arising from the answer to my question at:
haskell Either and Validation Applicative
My code is posted there.
It concerns the use of the *> sequencing operator instead of the <*...
- 491
-1
votes
1
answer
165
views
How to find Mutations for a reverse oriented gene(like pncA) from TB sequencing fasta file using biopython library in Python3?
To find a mutation like for S104R(from 2288681 to 2289241 for pyrazinamide), we have to first remove '-'(for stripping insertion/deletions if/any present in fasta file), then take reverse complement ...
- 59
0
votes
1
answer
56
views
Sorting dataset with abs() function
I am trying to run a gene set enrichment analysis following the vignette here:
http://yulab-smu.top/clusterProfiler-book/chapter7.html
I have been trying to use this particular code:
data(df, package=&...
- 43
0
votes
1
answer
392
views
Using grep with patternfile returns patterns (sequence names) not in patternfile
I am cleaning up sequencing data.
I have a file with reads (names) I'd like to find with grep and eventually remove.
The patternfile file is 219,721 lines long, with no duplicate entries. The sequence ...
- 5
1
vote
1
answer
499
views
R: Get index of first instance in vector greater than variable but for whole colum
I am trying to create a new variable in a data.table. It is intended to take a variable in the data.table and for each observation compare that variable to a vector and return the index of the first ...
- 55
5
votes
1
answer
3k
views
How does the messenger maintain the sequencing of the messages during chat and when users log in again?
I was asked this question in an interview and was unable to answer it.
How does FB messenger order the messages on user side when two messages are concurrent in order to avoid view difference in ...
- 2,227
2
votes
0
answers
241
views
Star index generation - 'std::bad_alloc' error
I was trying to generate a genome index using STAR index for mutant library 99,50 hours post fertilization (99H50) with the annotation form Lawson lab. The code I used is as follows:
module load STAR; ...
0
votes
1
answer
443
views
Script out of bounds in R
I am using a code based on Deseq2. One of my goals is to plot a heatmap of data.
heatmap.data <- counts(dds)[topGenes,]
The error I am getting is
Error in counts(dds)[topGenes, ]: subscript out ...