User: biolab

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biolab960
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Posts by biolab

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Answer: A: Command or Perl script for changing headers of multiple FASTA files in a specifi
... Please check the following commnds. First, run `cd AMY2b_Gene_folder/; mkdir new/`. Then, run `for f in *.fasta; do perl -e '$in=$ARGV[0]=~s/(.+?)\.fasta/$1/r; while (<>){if (/>/) {print ">$in\n"} else {print} }' $f > new/$f; done` ...
written 5 weeks ago by biolab960
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bowtie XA tag
... Hi, everyone, Bowtie has an XA tag (XA:i:), and its definition is as follows according to the manual. For a read with no reported alignments, `` is 0 if the read had no alignments. If [`-m`] was specified and the read's alignments were supressed because the [`-m`] ceiling was exceeded, `` equals ...
bowtie written 12 weeks ago by biolab960
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Comment: C: How to download raw data in batch from NCBI based on Series Accession number or
... Thank you very much, Istvan. The command you provided is really helpful! ...
written 3 months ago by biolab960
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Comment: C: HISAT2: does the parameter -k 1 means unique mapping?
... Thank you very much, genomax, these posts are very helpful. ...
written 3 months ago by biolab960
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Comment: C: HISAT2: does the parameter -k 1 means unique mapping?
... Hi, WouterDeCoster, thank you very much for your explanations. ...
written 3 months ago by biolab960
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HISAT2: does the parameter -k 1 means unique mapping?
... Hi, everyone, The `-k ` parameter in HISAT2 is explained by the following in the manual: **It searches for at most distinct, primary alignments for each read.** If I use `-k 1`, does it mean unique mapping? Thank you very much! ...
hisat2 written 3 months ago by biolab960 • updated 3 months ago by WouterDeCoster22k
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Comment: C: Is it necessary to include --known-splicesite-infile in HISAT2?
... Thanks a lot! genomax ...
written 3 months ago by biolab960
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Is it necessary to include --known-splicesite-infile in HISAT2?
... Hi, everyone, I am using HISAT2 for genomic mapping. In building index, I included `--ss` and `--exon` options, which store splicing site information. Then, is it necessary to include `--known-splicesite-infile` option in following HISAT2 mapping? I worry this option slow mapping without increase ...
hisat2 written 3 months ago by biolab960
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Comment: C: Is it OK to use --split-files option in fastq-dump when processing SE data?
... OK, genomax, thanks a lot for your explanations. I will try EBI-ENA. ...
written 4 months ago by biolab960
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Comment: C: Is it OK to use --split-files option in fastq-dump when processing SE data?
... Hi, genomax, could you please tell me the safe usage of fastq-dump? Thank you very much! ...
written 4 months ago by biolab960

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