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Gordon Smyth
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Recent Replies
Answer: Counting intronic reads in bulk RNA-seq
by
swbarnes2
13k
Are you sure this is appropriate for bulk RNASeq? I thought intronic reads for single cell were only counted in nuclear preps.
Answer: Single cell chemistry
by
swbarnes2
13k
Are you sure these samples are 10x? How likey is it that the sequencing group messed up and ran the samples wrongly?
Comment: How to deal with duplicated gene IDs in TCGA RNA expression data?
by
Vincent Laufer
★
2.8k
are they distinct transcript IDs but the same gene ID? can you provide any additional context?
Comment: SyntaxError (Perhaps you forgot a comma?) in snakefile when running FastQC.
by
Dhatri Badri
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0
that didn't work either
Answer: Why are some WES VCFs larger than others?
by
Vincent Laufer
★
2.8k
Hi @kermit and prash (and others)!
Nice discussion. I wanted to offer some **biological rationales** in addition to the technical reasons …
Answer: SyntaxError (Perhaps you forgot a comma?) in snakefile when running FastQC.
by
WouterDeCoster
47k
There is no `:` after `rule fastqc`
Comment: SyntaxError (Perhaps you forgot a comma?) in snakefile when running FastQC.
by
Dhatri Badri
•
0
sorry that was a typo while i was copying my code! I still get the same error
Comment: too many zeros in 16S rRNA amplicon sequencing data
by
andres.firrincieli
3.3k
You have too many ASV (40k) and I think this is a problem related to the denoising (DADA2) of NovaSeq 6000 sequencing data. Maybe this post…
Answer: SyntaxError (Perhaps you forgot a comma?) in snakefile when running FastQC.
by
Pierre Lindenbaum
154k
> fastq.gz".
what is the dot after `fastq.gz" ` ?
Comment: DownsampleSam
by
Pierre Lindenbaum
154k
1) I think this is just a warning
2) there must be another error displayed
3) look at samtools view --subsample
4) don't use loops but use…
Comment: ABySS genome assembler
by
npavliukovec
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0
Hello, yes, I tried it, but I have to do my home work on university's remote computer, unfortunatelly I go an error, when I try to use abys…
Comment: desgin a primer for CDS
by
yuxiang
•
0
how can you know the primer is not bind to other gene site? how can you desgin an experiment? I use the FISH to identify the gene, how abo…
Comment: desgin a primer for CDS
by
yuxiang
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0
sorry for my late reply, I am a student, my profossor ask me to dsgin a primer for the specific cDNA, I have solved now, thanks for your re…
Comment: vg: Mapping fewer reads to a genome graph than a linear reference
by
samuel.a.odonnell
▴
470
In this case filtering for quality might help correct for this overattributing feature?
Comment: ABySS genome assembler
by
GenoMax
129k
Did you see this guidance from ABySS manual: https://github.com/bcgsc/abyss#optimizing-the-parameters-k-and-kc
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