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Recent Replies
Comment: Kallisto and Salmon give different results
by
dsull
★
3.0k
Yes, you can use --fr-stranded or --rf-stranded depending on your library strandedness. I've never really seen a dramatic difference in res…
Comment: Kallisto and Salmon give different results
by
dsull
★
3.0k
They should give very similar results (but not identical), especially for bulk RNA-seq. It would be helpful for you to post some plots of t…
Comment: topGO error: Building most specific GOs ..... ( 0 GO terms found. )
by
park.seojeong2
•
0
Thank you for your rely!
You mean I have to change data uploaded as geneID2GO first, aren't you?
And you said "topGOData object should cont…
Comment: Assesing contaminants sequences from long genomic contigs
by
Antonio R. Franco
★
4.8k
you certainly focused my interest in using MetaMaps. I am reading the paper now.
Comment: Assesing contaminants sequences from long genomic contigs
by
Antonio R. Franco
★
4.8k
I am aware of minimap2 and its recent evolution ( a very active project indeed). But certainly, I rather use a truly and overall metagenomi…
Answer: Is there any tutorial page that tells you how to extract read count from illumin
by
ATpoint
60k
Based on the entry at NCBI https://www.ncbi.nlm.nih.gov/sra/?term=SRR5494706 this is a standard RNA-seq sample, not single-cell, so one col…
Comment: Assesing contaminants sequences from long genomic contigs
by
dthorbur
▴
190
Ah, I glossed over that aspect of the question. In that case, I would suggest `kraken2` might be the best fit given it's a kmer-based appro…
Comment: Conversion of gene symbol to refSeqID
by
cpad0112
20k
Please mind your genome versions (NCBI/build37.2 vs hg38 in OP)
Comment: Random Access Of Lines In A Compressed File Having A Custom Tabulated Format?
by
jena
▴
170
You are right, just use `tabix -p vcf` to set the expected format. I've [used this successfully][1] even on a file with just three columns …
Comment: Assesing contaminants sequences from long genomic contigs
by
GenoMax
115k
Do you have a related genome available that you could first use to see if you can pare the list of potential "contaminated" contigs down? A…
Answer: Conversion of gene symbol to refSeqID
by
vkkodali_ncbi
★
3.1k
You can try [NCBI Datasets](https://www.ncbi.nlm.nih.gov/datasets) for this. The web interface allows you to paste gene symbols for a speci…
Comment: Getting fastq files as the output of bowtie2
by
cpad0112
20k
bam2fastq/sam2fastq may help you.
Comment: RPKM, how to normalize for library size
by
ATpoint
60k
The library size is the sum of the column, so it takes it into account. The colSum is the effective library size that matters.
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