Moderator: lieven.sterck

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lieven.sterck4.2k
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Posts by lieven.sterck

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Comment: C: Blast script over multiple databases
... yes this will work (and congrats for solving it), but do consider using https://www.biostars.org/u/20598/ approach as that one is much more omni-applicable! ...
written 2 hours ago by lieven.sterck4.2k
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Comment: C: Blast script over multiple databases
... Do you need an output per DB or will one output over all DBs do it as well? What exactly do you mean with 'aliases'? ...
written 11 hours ago by lieven.sterck4.2k
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Comment: C: makeblastdb Error: ncbi::objects::CSeq_id::x_Init() - Unsupported ID type 119609
... Looks like there might be a problem with your input file (headers). Can you post the output of `grep '>' kraken2_blast | head` . Does this number/ID `1196094` appears in your fasta input file? ...
written 11 hours ago by lieven.sterck4.2k
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Comment: C: Interpreting HTSeq output file
... Did you not mention in a previous post you converted the bam file to sam format. If so then you need to change your htseq command accordingly. In any case the output of your countread.text file is not correct (looks like a kind of sam format?) ...
written 20 hours ago by lieven.sterck4.2k
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Comment: C: Interpreting HTSeq output file
... from which file is this the `head` ? It does not looks to be from `counread.text` , is it? If so then the output from your htseq command is not correct ...
written 21 hours ago by lieven.sterck4.2k
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Comment: C: Interpreting HTSeq output file
... 3 (5) words: "**never use excel**" ( for this) importing this kind of data files into excel can often cause unexpected behaviour. You're better of processing this file commandline in your linux environment. I assume you ran the previous steps commandline as well, no? Now for your specific issue: ...
written 22 hours ago by lieven.sterck4.2k
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Comment: C: HTSeq error while counting reads
... Please provide much more context for this issue. It's kinda hard to investigate this given the current information Eg. provide the exact cdmline you're trying to run. Post a glimps of the input files you are using, ... things like that. thx ...
written 2 days ago by lieven.sterck4.2k
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Answer: A: Using Salmon to quantify immature RNA?
... Sounds like an OK plan to me and I don't see any immediate issues with it. The only thing might be that you include some less-unique sequence (eg. repeats/TEs in introns) in the transcripts by including the introns but that should not be too much of an issue anyway. Tip: simply run `getfasta` fro ...
written 2 days ago by lieven.sterck4.2k
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Comment: C: Multiline Fasta To Single Line Fasta
... you can use the answer provided by https://www.biostars.org/u/375/ below. (it's not using tail) ...
written 2 days ago by lieven.sterck4.2k
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Comment: C: RNAseq sample never as A in last base
... If I understood correctly that last (extra base) does not get trimmed because it's 'rescued' by the previous bases I'm guessing that if you would put the window size to 1 with a low Qvalues it will get trimmed. ...
written 2 days ago by lieven.sterck4.2k

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