How to turn a column into a character string (to execute filterbyname.sh of the BBTools suite)
Hi all,
I'm not a super routine bash user and didn't find a solution for my problem via Google.
I want to extract FASTAs from a multi FASTA using filterbyname.sh of the BBTools suite. I found in the manual, that the names=file.txt input file should contain a character string.
I have a column of gene IDs. Alternatively, I already enclosed the IDs with double quotes. I´m trying to convert that column into a string. I tried the following commands and some variants, but it doesn't work.. :(
sed 's/\n/,/g' ensgene-of-interest.txt > ensgene-of-interest2.txt
cat ensgene-of-interest.txt | tr "\n" "\",\"" > ensgene-of-interest2.txt
cat ensgene-of-interest.txt | tr "\n" "\"" "," "\"" > ensgene-of-interest2.txt
Thanks a lot for your help :)
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you asked questions before on this forum that got answers. Comment or validate all your previous questions: determining read-depth of given size of genomic window via samtools ; Puzzling NCBI BLAST+ output after transcriptome assembly ; Trimming overrepresented sequence possible with Trimmomatic? ; Removing uncovered transcripts from multi FASTA reference file; etc...
Hi Pierre, I´m really sorry if I oversaw something. I double-checked the links you sent and I found that I either upvoted or answered to the comments. Is there an additional action I have to take?
validate the correct answers by clicking the green mark on the left .
Ella, why did you delete this post?
Because I triple-checked old posts of mine after Pierres comment, found that my problem was caused by re-doing an old mistake (not reducing very complex FASTA headers when mapping), felt stupid, and then deleted the post. :'D Sorry, very stressful thesis wrap-up times..
No worries. Please go ahead and delete this post again.