User: Afagh

gravatar for Afagh
Afagh70
Reputation:
70
Status:
Trusted
Location:
United states
Last seen:
1 month, 3 weeks ago
Joined:
1 year ago
Email:
f************@gmail.com

Posts by Afagh

<prev • 32 results • page 1 of 4 • next >
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Comment: C: concatenating different columns of different files bash script
... Works like a charm, could you help me to add the title of each file above each column? ...
written 9 weeks ago by Afagh70
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Comment: C: concatenating different columns of different files bash script
... Yes, I ran all the commands. I mean something like score1fromfile1 score1fromfile2 score1formfile3 score2fromfile1 score2fromfile2 score2formfile3 score3fromfile1 score3fromfile2 score3formfile3 But your command gives me: score1fromfile1 score2fromfile1 ...
written 9 weeks ago by Afagh70
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Comment: C: concatenating different columns of different files bash script
... Thank you, but I want the output to have one column for every file. Something like when we use `cut -f 5,11,17` ...
written 9 weeks ago by Afagh70
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Comment: C: concatenating different columns of different files bash script
... Thank you, but I want the output to have one column for every file. Something like when we use `cut -f 5,11,17` ...
written 9 weeks ago by Afagh70
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concatenating different columns of different files bash script
... I have a bunch of files, I want to concatenate 5th column of these files, but I don't know the number of files that find will find so I don't know what numbers I should put after cut -f file names 456Ecoli.bed, 568Ecoli.bed, ..... Each file has 6 columns The command doesn't work at all, I just w ...
bash written 9 weeks ago by Afagh70 • updated 9 weeks ago by Alex Reynolds22k
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Comment: C: Analysis of gene expression
... I didn't know it's confusing. I have only worked with metagenomics and metatranscriptomics datasets, so I didn't realize that what I'm doing is different from regular gene expression. ...
written 9 weeks ago by Afagh70
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Comment: C: Analysis of gene expression
... In metagenomics, we use a mixture of species as reference genome :) ...
written 9 weeks ago by Afagh70
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Comment: C: bash and awk code
... Hi Kevin, Your code works fine, but why `awk '/^Organism/{org=$0" "}; /,mir/{mir=$0}; /,[ATGC]*$/ {print org mir $0 "\n"}' test.data | sed 's/ ,/,/g'` doesn't work? Outputs: Organism: aau, Organism: aau, Organism: aau, ,mir162,,ATAAACCTCTGCATCCAG Organism: aau, ,mir162,,CGATAAACCTCTGCAT ...
written 9 weeks ago by Afagh70
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Answer: A: bash script for RNA seq analysis
... total=10 for (( i=1; i<${total}+1; i++ )); do script.bash RD${i}_R1.fasta RD${i}_R2.fasta # if you want to run a command with paired input mkdir RD${i} mv RD${i}_R1.fastq RD${i}/ mv RD${i}_R2.fastq RD${i}/ done ...
written 9 weeks ago by Afagh70
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Comment: C: bash and awk code
... I'm not very good at awk, but you can always do it step by step if you don't know how to do it in one command, for example something like this awk '/,mir*/{mir=$0}; /,[ATGC]*$/{printf mir $0 "\n"}' test.data > test1.data #adding the mir162 to the sequences awk '/^Organism/{org=$0" ...
written 9 weeks ago by Afagh70

Latest awards to Afagh

Scholar 9 weeks ago, created an answer that has been accepted. For A: bash script for RNA seq analysis
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: bash script for RNA seq analysis
Supporter 11 weeks ago, voted at least 25 times.

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