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Recent Replies
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 \
--sjdbGT…
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
Comment: Kraken2 is falsely assigning Klebsiella
by
SushiRoll
▴
110
Hi Philipp,
Thanks for your feedback. I found that 0.1 outputs includes most of the species the authors claim to be in their mock datase…
Answer: Filter vcf SNPs by sample GT value
by
Pierre Lindenbaum
157k
with GATK selectVariant https://gatk.broadinstitute.org/hc/en-us/articles/360037055952-SelectVariants a **JEXL** select expression (not te…
Answer: tximport error: vroom
by
Trivas
★
1.5k
Which version of Salmon are you using? According to the `tximport` documentation, older versions of `quant.sf` files from Salmon have comme…
Comment: Need help to setup a PGS pipeline
by
GenoMax
135k
You will need to provide at least one way for people to contact you. Please edit the post and add that information.
Answer: Kraken2 is falsely assigning Klebsiella
by
Philipp Bayer
7.9k
I've also had false positive hits with Kraken, usually a --confidence of 0.1 gets rid of *most* of them.
This paper deals a bit with the …
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