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Recent Replies
Comment: STAR Genome index Error
by
Ram
40k
Are you using a compute node or just the login node? If you're using a compute node, how much RAM did you request for allocation?
Comment: How do you validate and verify your pipeline's software updates?
by
kieran
•
0
No, just trying to start a discussion. It is documented that bioinformatics software testing is an important problem that the community is …
Comment: Understanding mother and father alleles in VCF file
by
Ram
40k
> a random person could appear as my relative just because has the same value of certain SNPs,
Yes. I recall there being a threshold, some…
Comment: How do you validate and verify your pipeline's software updates?
by
kieran
•
0
Testing could be done in a number of ways. Running to completion is definitely one form of it, but if it is just trying to make sure it is …
Comment: Commands to do the following in BCFtools or recommendations for another tool
by
Ram
40k
Yes, the first one is a good use case for bcftools annotate with the `-i` flag picking the appropriate variants to add the INFO/EXAMPLE tag…
Comment: Differentially Expressed Genes between two conditions (scRNA, single GEO dataset
by
bk11
★
1.4k
Your code `keep <- rowSums(counts(dds)) >=10` is not correct, please change it to-
keep <- rowSums( counts(dds) >= A ) >= B
dds <-…
Comment: STAR Genome index Error
by
Prasanna
•
0
```
STAR --runMode genomeGenerate \
--genomeDir GRCh38.79.chrom1 \
--genomeFastaFiles genome/Homo_sapiens.GRCh38.dna.chromosome.1.fa \
--sj…
Comment: STAR Genome index Error
by
Trivas
★
1.5k
It's actually 12 - the creators have said on a forum to take the floor when rounding `log2(GenomeLength)/2-1` which isn't well represented …
Comment: How to check RNAseq support for annotated genes?
by
BioinfoBee
•
0
@michaeld Thanks again!, Just curious, if its possible to align transcripts to the genic regions only using the gene annotation gtf/gff fil…
Comment: STAR Genome index Error
by
biofalconch
★
1.0k
From the documentation
> For small genomes, the parameter --genomeSAindexNbases must to be scaled down, with a typical
value of min(14, lo…
Comment: STAR Genome index Error
by
Trivas
★
1.5k
Agreed it's a memory problem, I'm wondering if using the appropriate `genomeSAindexNbases` value helps in this case.
Comment: ATAC-Seq and RPKM
by
Yogi
▴
40
This is what you're looking for.
Check out this very famous tool `DeepTools`.
https://deeptools.readthedocs.io/en/2.4.0/content/tools/b…
Comment: Extract Loci based on the snps number
by
Yogi
▴
40
I think this may be what you're looking for.
You can subset by regions.
https://samtools.github.io/bcftools/bcftools.html#view
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