User: Mitra

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Mitra0
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Posts by Mitra

<prev • 17 results • page 1 of 2 • next >
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Comment: C: Problem with installing SeqPrep from GitHub
... I think installation by anaconda is easier. conda install -c bioconda seqprep ...
written 7 days ago by Mitra0
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Comment: C: Problem with installing SeqPrep from GitHub
... Hi, I tried to use install it same way... but getting error [medsmit@login2.marc1 SeqPrep]$ git checkout clang-patch error: pathspec 'clang-patch' did not match any file(s) known to git. Can you please help? Thanks. Mitra ...
written 7 days ago by Mitra0
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Comment: C: Read count from a batch of fastq.gz files
... Yes I described above two different ways of Read count from a batch of fastq.gz files ..out of which `$((`wc -l`/4))` don't work (rather I must say not getting expected or correct result) when applied to zip files. So I assume this is something to do with the zip files ..and try to understand how t ...
written 11 days ago by Mitra0
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Comment: C: Read count from a batch of fastq.gz files
... Also when I am checking with one file I get exact match..but somehow above command not working.. grep "@M" RIFA3D26_S20_L001_R2_001.fastq |wc -l 145592 grep "@M0369" RIFA3D26_S20_L001_R2_001.fastq |wc -l 145592 This confirms that all the reads have same name. Also with line cou ...
written 11 days ago by Mitra0
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Comment: C: Read count from a batch of fastq.gz files
... No ..thats not the fact ..and yes they all named as M03691 as much I can see. ...
written 12 days ago by Mitra0
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Comment: C: Read count from a batch of fastq.gz files
... Great works thanks..don't know why zgrep didn't come to my mind. But still I really wonder why wc -l`/4 didn't work. Definitely all these fastq files have 4 lines. ...
written 12 days ago by Mitra0
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Read count from a batch of fastq.gz files
... Hi, How can we do Read count from a batch of fastq.gz files. Obviously if we unzip it then it is easy by grep. But what is the best way to do without unzipping. I tried this for a batch of files: for i in `ls RIF*.fastq.gz | sort`; do zcat $i | echo $((`wc -l`/4)) ; done Gives me resu ...
next-gen sequencing written 12 days ago by Mitra0 • updated 12 days ago by Devon Ryan70k
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Comment: C: Labelling sequences within fasta files according to sample name.
... Thank you very very much shoujun.gu you saved my day :) A BIG Thank you ...
written 17 days ago by Mitra0
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Comment: C: Labelling sequences within fasta files according to sample name.
... yes there is correlation ...File names are same as sample name which I want to insert after > for each sequence in each multifasta file. These files are already demultiplexed and adapter+barcode removed. Then I stitched them using fastq join (within qiime 1.1.9) and converted them to fasta from ...
written 17 days ago by Mitra0
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Comment: C: Labelling sequences within fasta files according to sample name.
... Hi shoujun.gu, should I run this in a for loop for multiple input file? I have over 100 fasta files to run... Can you please suggest?Thanks Mitra ...
written 17 days ago by Mitra0

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