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Popular Question to
Omics data mining
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Pierre Lindenbaum
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benformatics
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Recent Replies
Answer: Adding MBC/UMI RX tag to read name
by
Christian
▴
20
# this script takes a BAM file and moves the UMI tag from the RX tag
# and appends it to the read name
# argument 1: input fi…
Comment: Is it ok to trim assembled paired-end fastq files with cutadapt 3.4 ?
by
GenoMax
127k
> I´m concatenating two sets of files before trimming to remove
> sequences from both of them
That only makes sense if it is the same samp…
Comment: getting coding exon information from Ensembl API
by
Sarah
▴
30
Why does this bother you !
Who is you ? the admin of this forum ?
we are here to learn, not to be watched. Dont comment my post again ple…
Comment: Is it ok to trim assembled paired-end fastq files with cutadapt 3.4 ?
by
Bengisu
•
0
Thank you for sharing.
I´m concatenating two sets of files before trimming to remove sequences from both of them. But, I don´t know if it i…
Comment: getting coding exon information from Ensembl API
by
Pierre Lindenbaum
153k
[again, and again and again, so many questions and no validation][1]
[1]: https://www.biostars.org/u/67462?active=posts
Comment: Seeking Jr. Bioinformatician Position
by
santos48
▴
40
Thank you so much, I will also add my e-mail.
Comment: Seeking Jr. Bioinformatician Position
by
GenoMax
127k
There is no way for people to contact you (via personal messages or otherwise) on this forum. You may want to look at alternate avenues if …
Comment: Snakemake vs Nextflow Upcoming bioinformatics Project
by
colindaven
4.5k
Don't worry about groovy too much. I have been writing productive nextflow pipelines for a couple of years and still haven't learned much i…
Comment: Java -xmx option does not limit memory usage in the ImputePipelinePlugin?
by
lcj34
▴
220
Does the amount of memory keep increasing, or does it start high and remain stable? Do you have a log file you can post? That may give us…
Comment: 10x 3' library creates R1 and R2 fastq files with the same read length
by
GenoMax
127k
> Then, we can just effectively ignore everything from bp 29 onwards?
Yes.
Comment: 10x 3' library creates R1 and R2 fastq files with the same read length
by
bompipi95
▴
120
Hi! Jusrt so that I understand this correctly, for the 10x v3 libraries sequenced on Novaseq, does it mean that if R1 is 150bp and looks li…
Comment: Java -xmx option does not limit memory usage in the ImputePipelinePlugin?
by
GenoMax
127k
Based on the program name `run_pipeline.pl` this appears to be a perl script. Option you are referring to is for `Java`. Is that perl scrip…
Comment: Is it ok to trim assembled paired-end fastq files with cutadapt 3.4 ?
by
GenoMax
127k
> So, I prefer to work assembled fastq files into one fastq rather than
> two.
What does this mean? Are you concatenating two sets of file…
Comment: What is exactly meant by "GENCODE TSS"?
by
ntsopoul
▴
40
checkout: chipseeker package
there is a function which gets you the tss
getPromoters(TxDb=txdb, upstream=3000, downstream=3000)
as you c…
Comment: SRA Taxonomy Analysis - difference between tables and web
by
GenoMax
127k
> Apparently it is ok for some accessions
In that case, your best bet is to contact NCBI help desk with examples of what works and what do…
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