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updated 7 hours ago by
Gordon Smyth
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written 14 hours ago by
Apprentice
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updated 6 months ago by
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written 8.3 years ago by
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updated 6 hours ago by
Billy Rowell
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written 18 hours ago by
jahnreinhard.ringger
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21 hours ago by
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17 hours ago by
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1 day ago by
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updated 1 day ago by
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1 day ago by
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updated 1 day ago by
colindaven
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written 2 days ago by
alexandrakortsi
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updated 2 days ago by
Jouni Sirén
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written 7 days ago by
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updated 16 hours ago by
Paulo
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written 11.2 years ago by
Istvan Albert
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2 days ago by
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updated 2 days ago by
i.sudbery
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written 3 days ago by
Alana Conceição Maia Lessa
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updated 2 days ago by
colindaven
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written 3 days ago by
gulin
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updated 2 days ago by
GenoMax
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written 2 days ago by
paulanavarrete116
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updated 1 day ago by
lieven.sterck
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written 6 days ago by
Jl
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updated 18 hours ago by
Istvan Albert
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written 3 days ago by
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updated 3 days ago by
lieven.sterck
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written 3 days ago by
Naila
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3 days ago by
SomeOne
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updated 3 days ago by
yura.grabovska
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760
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written 3 days ago by
zhang616123
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updated 2 days ago by
Bastien Hervé
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written 3 days ago by
Jonathan Yoou
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3 days ago by
soledad.esteban
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updated 3 days ago by
colindaven
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written 4 days ago by
ZuelTech
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updated 4 days ago by
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written 6 days ago by
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Recent Replies
Answer: Issues with T2T in pigeon prepare from isoseq
by
anbayega
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0
Got the same error using T2T. I will wait to see if there's a quick fix.
Comment: Extract length of sample sequence from vcf
by
Billy Rowell
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If you don't want to mess with compiling bleeding-edge bcftools, you could write the same thing in awk. There's no need to filter out the …
Answer: How to obtain TPM data after batch effect correction from count data obtained us
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Gordon Smyth
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I would be using divided counts for transcript-level analyses from RSEM, and using log-CPM from the divided counts for clustering, for the …
Answer: Missing short indels from vcf
by
LauferVA
4.7k
Hey @kbranger ,
IIUC, you have a ~7 bp deletion visible in IGV (with a 7D CIGAR string and ~17–20× depth) that disappears after bcftools…
Comment: Modify read groups in BAM file
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1769mkc
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is this onboard or basespace or ICA? dragen
Comment: MultiQC_report
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GenoMax
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That is pretty odd. Like you were advised above you could try to open an issue with the devs. I don't think I have ever seen this problem. …
Answer: Facing issue with output of nextflow pipeline
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mmhryc
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With nextflow you don't want to manage paths manually. Instead of creating a hardcoded path you should let it output the results into whate…
Answer: Choosing the best clustering method for a certain methylation data
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[Affinity propagation][1] is the answer to all my clustering needs
[1]: https://utstat.toronto.edu/reid/sta414/frey-affinity.pdf
Comment: Modify read groups in BAM file
by
Alex
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0
Thanks Istvan, this seems like a reasonable enough solution that could be scripted across large batches of files. I'll give it a shot. Was …
Comment: MultiQC_report
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AIMAR
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No I don't, when I said errors I mean it shows 267 samples for the adapter content while I just have 50 samples of paired-end read = 100 re…
Comment: MultiQC_report
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150k
> in this report multiqc missed 3 samples (6 reports ) and still made the error with the adapter content.
Do you have any oddities in samp…
Answer: Extract length of sample sequence from vcf
by
Billy Rowell
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500
This is hacky and definitely not prod ready, but if the goal is to get the length and not the sequence, you could use bcftools/paste/bc to …
Comment: Extract length of sample sequence from vcf
by
LauferVA
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you probably want to be working wihta bam file for this ..
Comment: MultiQC_report
by
AIMAR
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![enter image description here][1]
Here is the screenshot, in this report multiqc missed 3 samples (6 reports ) and still made the error…
Comment: Extract length of sample sequence from vcf
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Istvan Albert
102k
Once you slice the reference genome, the positions in the VCF won't match the reference. For your method to work you would need to shift th…
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