User: biolab

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Posts by biolab

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How to highlight regions in RNA second structure
... Dear All, I have many miRNA precursor sequences, and it is easy to get the pictures of their secondary structures in batch using RNAFOLD, MFOLD or other tools. My problem is: how to highlight or label a region (for example, miRNA or miRNA*) in the RNA structure graph by customized color? Thank you ...
rna second structure written 16 months ago by biolab1.1k
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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 21 months ago by biolab1.1k
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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 23 months ago by biolab1.1k
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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 23 months ago by biolab1.1k
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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 24 months ago by biolab1.1k
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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 24 months ago by biolab1.1k
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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 24 months ago by biolab1.1k • updated 24 months ago by WouterDeCoster39k
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Comment: C: Is it necessary to include --known-splicesite-infile in HISAT2?
... Thanks a lot! genomax ...
written 24 months ago by biolab1.1k
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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 24 months ago by biolab1.1k
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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 2.1 years ago by biolab1.1k

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