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mapsembler • reset11
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written 3.1 years ago by
pierre.peterlongo • 600
• updated
2.7 years ago by
shelkmike • 20
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Recent Replies
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C: featureCounts reports zero counts when using GTF Repeatmasker track from UCSC an by
Gema Sanz • 30
Thanks for your answer h.mon! In Bowtie2 I used default mode (search for multiple alignments, rep...
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C: VIew reads sorted by name in IGV by
nchuang • 160
I think dariober asked me the same thing and I explained it very briefly. I am just using IGV for...
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A: Which package to use for RPKM/FPKM RNA-seq counts? by
Renesh • 870
DESeq2 is a good package for DEG analysis in R. https://bioconductor.org/packages/release/bioc/ht...
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C: Xenopus genome files for RNAseq by
Ron • 600
Try checking the links I pasted above.These are xenbase links only.
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C: fpkm to tpm conversion by
Renesh • 870
You can still calculate TPM from RPKM/FPKM values.You need to have information about a total numb...
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C: fpkm to tpm conversion by
Renesh • 870
Please, read this article for basic calculation, http://bioinfogeek.over-blog.com/2017/09/gene-e...
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C: fpkm to tpm conversion by
Renesh • 870
http://bioinfogeek.over-blog.com/2017/09/gene-expression-units-explained-rpm-rpkm-fpkm-and-tpm.html
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C: featureCounts reports zero counts when using GTF Repeatmasker track from UCSC an by
h.mon ♦ 8.6k
Probably featureCounts is discarding multi-mapped reads, hence zero counts for repeats. You have ...
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C: Technical replicates in RNAseq by
WouterDeCoster ♦ 21k
You are very right - what my example didn't include is variability due to sampling (a Poisson dis...
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C: Technical replicates in RNAseq by
Macspider • 1.4k
I couldn't agree more. Basically, on the theoretical level I agree with @WouterDeCoster but on th...
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A: Bosst configure error by
mike • 0
I had the same problem and could not get around it until I installed the sqlite dev libraries.
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C: SNPs in population; vcftools by
Kevin Blighe • 930
Yes, they appear to generally have similar frequencies across each population. The only differenc...
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