User: S AR

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S AR50
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50
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Location:
Pakistan
Last seen:
1 day, 10 hours ago
Joined:
3 years, 8 months ago
Email:
a*********@gmail.com

Posts by S AR

<prev • 53 results • page 1 of 6 • next >
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Answer: A: Getting unusual characters while generating output files in a bash script
... The error was resolved using : #dos2unix sed `echo "s/\r//"` ../pre_xdr_20_batch_run.sh > pre_xdr_20_batch_run.sh Secondly I found an answer to run it in a loop : https://bioinformatics.stackexchange.com/questions/5635/how-to-run-same-command-on-multiple-files/5640?noredirect=1#comment ...
written 1 day ago by S AR50
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Comment: C: Getting unusual characters while generating output files in a bash script
... The only thing that change in the read group header will be tID and tSM. that will be the file names. ...
written 2 days ago by S AR50
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Comment: C: Getting unusual characters while generating output files in a bash script
... And if anyone suggest a better way of doing it like a loop that can get file name from a list? ...
written 2 days ago by S AR50
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Comment: C: Getting unusual characters while generating output files in a bash script
... Yes there are first i'm trying to do this if i get success that i make a loop or something. And i ran : dos2unix ../pre_xdr_20_batch_run.sh It outputted: dos2unix: converting file ../pre_xdr_20_batch_run.sh to Unix format... But i found no change.. ...
written 2 days ago by S AR50
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6 follow
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Getting unusual characters while generating output files in a bash script
... Hi i im trying to run one command on mutliple files so i made a .sh script to do it: bwa mem -M -R '@RG\tID:ERR040140\tLB:2517707\tPL:ILLUMINA\tPM:HiSeq2000\tSM:ERR040140' ../ref/M._tuberculosis_H37Rv_2015-11-13.fasta ERR040140_* > ERR040140.sam bwa mem -M -R '@RG\tID:ERR046796\tLB ...
sh bash unix linux written 2 days ago by S AR50
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Comment: A: How to separate a strain of MTB drug wise?
... Hi @rizoic, im still unable to find the solution if you can please help me? ...
written 17 days ago by S AR50
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Comment: C: is there a way to get SRA info (Paired Library, Sample id, Seq Tech... etc) usin
... I tried from your previous command the following: cat ../MDR.txt | parallel -j 4 "esearch -db sra -query {} | efetch --format runinfo" It is f=giving me the results but it is again again getting the headers for each entry as well. Is there a way to get the headers once only in the start and th ...
written 23 days ago by S AR50
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Comment: C: is there a way to get SRA info (Paired Library, Sample id, Seq Tech... etc) usin
... As by reading i understand that you have made a function with the name mymeta. but this can be run in linux directly i guess. should i make it a python script? does python have builtin esearch efetch module?? As when i tried to run it as it is by making a bash script it is saying: /bin/bash: mymet ...
written 23 days ago by S AR50
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Comment: C: is there a way to get SRA info (Paired Library, Sample id, Seq Tech... etc) usin
... And now i looked it that if i remove that coloumn cutting command it gives me the info table. Thanks Again ATpoint for help. Can you please explain the above command ? what is mymeta? ...
written 23 days ago by S AR50
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Comment: C: SRA files bulk downloads
... Ye kind of. I just have to break my list into 3 halves and than it is working but still it is missing few IDS but i can manage those few manually. ...
written 23 days ago by S AR50

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