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1500 questions
3
votes
1 answer
How to filter Ensembl cDNA and ncRNA FASTA files by primary assembly?
I'm currently performing differential expression analysis using alignment-free quantification using Kallisto. To do this, I need to create a Kallisto index using Ensembl's cDNA and ncRNA annotations available at the following two…
michaelmccarthy404
- 131
- 2
3
votes
1 answer
BioMart returns one more item
I am supplying 30 ensembl ids into BioMart, but somehow it returns 31 result. What is going wrong here?
Here you can see the code:
library('biomaRt')
mart <- useDataset("mmusculus_gene_ensembl", useMart("ensembl"))
genes <- rownames(mat)
G_list <-…
Nikita Vlasenko
- 2,558
- 3
- 26
- 38
3
votes
2 answers
10X Illumina demultiplexing sample sheet issue
Also posted on biostars.
I am trying to use cellranger or bcl2fastq to convert the .bcl files that I got from single cell analysis run into fastq files for further analysis. I needed to generate sample_sheet.csv and so I used the following…
Nikita Vlasenko
- 2,558
- 3
- 26
- 38
3
votes
1 answer
Estimating computing resources needed for a GWAS?
One of my dissertation papers is going to involve a GWAS. I have never actually run a GWAS before, and do not know how to estimate the computing resources I need for it. I asked someone on my committee who said "it's all guesswork" but I don't even…
bluemouse
- 195
- 4
3
votes
1 answer
Cufflinks Error: sort order of reads in BAMs must be the same
I am running Cufflinks for transcriptome assembly using the .bam file generated by Hisat2. I tried both bam and sorted bam files
cufflinks --no-update-check -o ./ -p 15 accepted_hits.bam
it gives the following error:
Error: sort order of reads in…
SBDK8219
- 195
- 8
3
votes
2 answers
Subset data frame by similar elements from rows and column between two data frames
My first data frame whose first column i intend to use which is PATIENT_ID
PATIENT_ID SEX RACE FAB AGE BM_BLAST_PERCENTAGE WBC
TCGA-AB-2805 Male WHITE M0 77 67 92
TCGA-AB-2822 Male WHITE M0 65 99 2.9
TCGA-AB-2831 Male …
kcm
- 1,804
- 12
- 27
3
votes
1 answer
How to download gene expression data from NCBI gene database
In the NCBI gene database, I can add the expression tracks (circled in picture blow) through 'Tracks' button, but How I can download the expression data directly, not just look the picture?
YudongCai
- 31
- 1
3
votes
1 answer
How to read gene regulatory network edge list files?
The following is an excerpt from an edge list file from the Gene Regulatory Database, YeastNet v3
YML100W YMR261C 5.73968189451551
YDR074W YML100W 5.73143623470086
YDR074W YMR261C 5.72385204041689
YML106W YMR271C 5.64698433340441
YGR240C YMR205C…
Kunal24
- 139
- 1
3
votes
2 answers
Pepsin digest (cleavage) does not work using RE?
Aim is to code the theoretical peptic cleavage of protein sequences in Python. The cleavage (cutting) rule for pepsin is: 1234^567. This is a position, ^ stands for the cleavage point.
There are rules that it mustn't have at all and rules where it…
Nadecho Holme Attaveesin
- 105
- 6
3
votes
1 answer
Digisome generation
I scoured and searched the web for some implementation of digisome creation, but I had a hard time finding any good source code.
By digisomes, what I mean is images with chromosomal masks/borders that have been simulated. I am seeking this because…
Jonathan
- 341
- 2
- 10
3
votes
1 answer
Impute phenotype under some constraints
Errors happen frequently in the lab and I got one sample that we mixed one important information (the region of the sample) between two samples. Now we don't know which sample is from which region, but we know all the other variables (Date of the…
llrs
- 4,693
- 1
- 18
- 42
3
votes
1 answer
How to retrieve the yeast locus tag from uniprot via sparql?
Let's say I want to retrieve the yeast-specific identifier for a certain protein, in the example below it will be P00330 which I would like to link to YOL086C.
When I go to uniprot's sparql UI and type
PREFIX up:
Cleb
- 743
- 7
- 18
3
votes
1 answer
Syntenic gene browser
I found that there is a Syntenic gene browser at GEvo. Do anyone know where could I find a similar browser for a local installation?
user977828
- 453
- 3
- 9
3
votes
1 answer
How to use C++ htslib to read VCF contig name and size?
A typical VCF file has:
##contig=
##contig=
I would like to use htslib in C++ to read it. My attempt:
htsFile *fp = bcf_open("my.vcf", "r");
bcf_hdr_t *hdr = bcf_hdr_read(fp);
In…
SmallChess
- 2,699
- 3
- 19
- 35
3
votes
1 answer
gffread: GFaSeqGet errors on coordinate overhang
Disclaimer: I had this issue posted on Tuxedo Tools users group and shared it on Twitter, but could not get an answer to this from the developers, nor find documentation of this issue online. So, I'll share my solution here below and see if some of…
aechchiki
- 2,676
- 11
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