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Answer: Adding MBC/UMI RX tag to read name
Comment: Is it ok to trim assembled paired-end fastq files with cutadapt 3.4 ?
Transforming And Manipulating Color Space Reads
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Comment: 10x 3' library creates R1 and R2 fastq files with the same read length
The Biostar Handbook. A bioinformatics e-book for beginners.
The Biostar Handbook. A bioinformatics e-book for beginners.
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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
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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
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santos48
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Thank you so much, I will also add my e-mail.
Comment: Seeking Jr. Bioinformatician Position
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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 …
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colindaven
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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…
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lcj34
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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
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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?
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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 ?
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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"?
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ntsopoul
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checkout: chipseeker package there is a function which gets you the tss getPromoters(TxDb=txdb, upstream=3000, downstream=3000) as you c…
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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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