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kissDE: How do I use diffExpressedVariants with some zero counts in my data?

R diffexpressedvariants rna-seq kissde written 4 months ago by Zoe • 0

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Error in running "diffExpressedVariants" function in kissDE R package

kissplice snp kissde written 12 months ago by c.evang • 10 • updated 9 months ago by vincent.lacroix • 40

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Error running KissDE

kissde kissplice written 11 months ago by c.evang • 10

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Recent Replies

A: The difference between okay.cds and okay.fasta produced by tr2aacds by gilbert.bionet • 60
The okayset/ of files you ask about from tr2aacds contain the subset of your input transcripts t...
A: Bash: find duplicates based on 2 columns and keep duplicate with lowest value in by Kevin Blighe • 940
This is a somewhat cheeky way of doing it. Re-using your code, I then numerically sort the data ...
C: How to filter SNPs after Freebayes, if at all, in a fungal haploid genome alignm by Brian Bushnell ♦ 14k
Coverage is pretty variable so even if the average is, say, 300x I still don't see a good reason ...
C: samtools: error while loading shared libraries: libbz2.so.1.0: cannot open share by Devon Ryan ♦ 70k
Put `conda-forge` second, after `bioconda`.
A: HtSeq count error by Ron • 600
The bam file is working fine with older HTSEQ version 0.6.1, which I was using previously. So I r...
C: How to filter SNPs after Freebayes, if at all, in a fungal haploid genome alignm by Lina F • 100
I have >100X coverage, so I should be ok on that front. I will take a look at IGV. Ultimately...
C: gene set enrichment analysis for continuous phenotype by Ron • 600
Can you explain more on the continuous outcome?
A: Advice on primer ordering for 16s + ITS sequencing by samdegregori • 0
bump
C: Introducing FilterByTile: Remove Low-Quality Reads Without Adding Bias by fusion.slope • 120
Hi br.m, sorry for the late reply. Basically i did a bash script removing the tiles in the red c...
A: gc content file for human genome large and difficult to parse into separate chro by igor • 4.5k
You can use `bedtools nuc` to get GC content at any resolution. The input BED file that defines t...
C: Need help reading FASTQ file by jrj.healey • 2.3k
Yeah I should probably add the caveat that I'm assuming a perfect input, but I would hope if some...
A: gc content file for human genome large and difficult to parse into separate chro by Alex Reynolds ♦ 20k
Use [BEDOPS][1] tools to convert, split and manipulate genomic interval datasets: Your first fil...

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