User: cschu181
cschu181 • 1.2k
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Posts by cschu181
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... Look at the FastQC report - if it shows Adapter contamination there (Adapter and Overrepresented Sequences) then you should run Trimmomatic using the default settings on their webpage and see what that does (run FastQC again on the trimmed reads). You might need to check which adapter file to use. A ...
written 1 day ago by
cschu181 • 1.2k
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... You should be able to generate the gene_regions file from the gtf (e.g. using bedops as suggested in https://www.biostars.org/p/56280/). For the gene_alias file you could try "cheating" and just give a tab-separated file containing one row for each gene with all three columns having the same Ensembl ...
written 1 day ago by
cschu181 • 1.2k
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... 1. You can trim your exome reads with Trimmomatic just as you can do with WGS reads.
2. I wouldn't worry about the base sequence content of the first 10bp. That is the typical picture and in exome seq, which is more biased than WGS, it is even less alarming.
3. -t is not needed for viewing unles ...
written 1 day ago by
cschu181 • 1.2k
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Comment:
C: h5 file of cell ranger
... https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/h5_matrices says non-zero UMI counts, doesn't mention normalization at all. ...
written 1 day ago by
cschu181 • 1.2k
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... What is the next downstream step? I am just wondering whether the 0-coverage positions are really needed to be present or could be inferred by whatever tool/script/step happens next. ...
written 17 days ago by
cschu181 • 1.2k
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... Maybe ask those detailed questions to one of the Trimmomatic devs (Tony Bolger is usually quite helpful -- you can find his details on
the same webpage that also has the Trimmomatic documentation). If you do, please don't forget to share your newfound knowledge here.
Also, slightly out of topic: I ...
written 19 days ago by
cschu181 • 1.2k
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... Sorry, I didn't want to sound harsh. I agree with that sentiment, OP might not know about available tools, so of course suggesting seqtk makes sense!
Concerning your remark about the use of a set. We don't expect duplicates, but using a list, as you suggest, requires linear search to check for eac ...
written 19 days ago by
cschu181 • 1.2k
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... While I agree with "don't reinvent the wheel", I also appreciate when people try and solve such things by their own - how else are you supposed to learn? ...
written 19 days ago by
cschu181 • 1.2k
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... In your remove file, do the sequence ids still have the fasta ">" prepended? ...
written 20 days ago by
cschu181 • 1.2k
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... Just a hunch, does your read_ids.txt contain the "@" at the start of the fastq identifiers? ...
written 23 days ago by
cschu181 • 1.2k
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