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C: snpEff assigned all variants as modifier intergenic
A: Problem in indexing toplevel genome with HISAT2
C: The Biostar Handbook. A bioinformatics e-book for beginners.
Answer: Error with BiocParallel. No barcodes files found
Error with BiocParallel. No barcodes files found
Comment: How do we do quantification using stringtie merge option for all the merged samp
Answer: bcftools view error: the tag "mis" is not defined in the VCF header
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Recent Replies
Comment: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
by
GenoMax
142k
> only give me partial results It is possible that not every Ensembl ID is going to convert to Entrez ID. Have you tried: https://www.b…
Comment: BAM to Bedgraph creating an empty file
by
raphael.B
▴ 520
You have a space in your reference path. Not sure it's intended?
Comment: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
by
Anya
• 0
Do you have any recommendations of such sources or how to search for them? I'm a newbie and I need to convert GRCh38 Ensembl IDs to Entrez …
Comment: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
by
Shred
★ 1.4k
Genecards added a footer saying that >SCRAPING AND OTHER AUTOMATED DOWNLOAD AND USE OF GENECARDS DATA STRICTLY PROHIBITED While this is …
Comment: perl Error - needLargeMem Bigwig
by
marco.barr
▴ 130
I managed to correct and solve the problem. It was due to issues with memory parameter settings on different login nodes. Additionally, I h…
Answer: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
by
Anya
• 0
Here's a slightly changed version of this script. I changed line 42 from `'title':'NCBI Entrez Gene'` to `'title':'NCBI Gene'` ). And…
Comment: How do we do quantification using stringtie merge option for all the merged samp
by
Varsha
• 0
Thank you for the detailed explanation.
Answer: How can run cd-hit-est with a clstr threshold less than 0.8?
by
Asaf
10k
For future reference The 0.8 identity threshold for EST (nucleotides) is hardcoded. However, there's an option to use `-D` (distance) in…
Answer: Tools for chromosomal aneuploidy detection
by
a.alnawfal.1992
▴ 260
As far as I know, all the tools utilised control group to compute the z score for chromosomal aneuploidy. but is your goal detect chromosom…
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2
by
Sara
▴ 30
I used Seurat, and in Seurat, I have gene names (which some are with gene-symbols and some with ENSG ids). Then I did Pseudobulk. how can …
Comment: How to decrease the motif score?
by
ATpoint
82k
So you scan the entire genome and got nothing significant? Is that the issue?
Comment: perl Error - needLargeMem Bigwig
by
b.contreras.moreira
▴ 200
A quick search suggests the problem is your empty input file? See <https://biostar.galaxyproject.org/p/6794>
Comment: Invalid CIGAR after using bam clipOverlap
by
MboiTui
▴ 20
ooh good pickup. Might not be the problem but definitely not helping. Will re-run with streamlined workflow and with double quotes and see …
Comment: Invalid CIGAR after using bam clipOverlap
by
Pierre Lindenbaum
162k
may be not the problem but why this ` RG:Z:H7J22DRX3.${lane}-1C23074F ` in the RG. you're using single quotes with bwa-mem and it won't …
Comment: Invalid CIGAR after using bam clipOverlap
by
MboiTui
▴ 20
Hello Pierre, Thanks for your reply and insight. with samtools view | grep using the erroneous CIGAR string I get: A00152:841:H7J22D…
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