User: Afagh
Afagh • 70
- Reputation:
- 70
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- Location:
- United states
- Last seen:
- 3 months ago
- Joined:
- 1 year, 7 months ago
- Email:
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Posts by Afagh
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0
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... Works like a charm, could you help me to add the title of each file above each column? ...
written 9 months ago by
Afagh • 70
1
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790
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... 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 months ago by
Afagh • 70
0
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2
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790
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... 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 months ago by
Afagh • 70
0
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790
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... 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 months ago by
Afagh • 70
7
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790
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... 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 ...
written 9 months ago by
Afagh • 70
• updated
9 months ago by
Alex Reynolds ♦ 24k
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399
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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 months ago by
Afagh • 70
0
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399
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Comment:
C: Analysis of gene expression
... In metagenomics, we use a mixture of species as reference genome :) ...
written 9 months ago by
Afagh • 70
0
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2
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946
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2
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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 $0 "\n"}' test.data | sed 's/ ,/,/g'` doesn't work?
Outputs:
Organism: aau, Organism: aau,
Organism: aau, ,mir162,,ATAAACCTCTGCATCCAG
Organism: aau, ,mir162,,CGATAAACCTCTGCAT ...
written 9 months ago by
Afagh • 70
3
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1.1k
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... total=10
for (( i=1; i<${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 months ago by
Afagh • 70
1
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2
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946
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2
answers
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 months ago by
Afagh • 70
Latest awards to Afagh
Scholar
9 months ago,
created an answer that has been accepted.
For A: bash script for RNA seq analysis
Teacher
9 months ago,
created an answer with at least 3 up-votes.
For A: bash script for RNA seq analysis
Supporter
9 months ago,
voted at least 25 times.
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