extract fasta sequence with the help of bedtools getfasta
Can I download the reverse strand by bedtools getfasta. If I have reverse strand coordinates.
X 154401758 154402841 ENST00000014935 ENSE00001200781 9
X 154402942 154403190 ENST00000014935 ENSE00000678409 8
X 154403269 154403381 ENST00000014935 ENSE00003549633 7
X 154403522 154403622 ENST00000014935 ENSE00000678413 6
X 154404828 154404914 ENST00000014935 ENSE00003790806 5
X 154404995 154405083 ENST00000014935 ENSE00000678418 4
X 154405434 154405655 ENST00000014935 ENSE00001450968 3
X 154409112 154409196 ENST00000014935 ENSE00001050508 2
X 154409418 154410039 ENST00000014935 ENSE00001050512 1
I just want to extract the sequence in reverse orientation like when i used bedtools getfasta then it gives fasta sequence in reverse direction :
X 154402841 154401758 ENST00000014935 ENSE00001200781 9
X 154403190 154402942 ENST00000014935 ENSE00000678409 8
X 154403381 154403269 ENST00000014935 ENSE00003549633 7
X 154403622 154403522 ENST00000014935 ENSE00000678413 6
X 154404914 154404828 ENST00000014935 ENSE00003790806 5
X 154405083 154404995 ENST00000014935 ENSE00000678418 4
X 154405655 154405434 ENST00000014935 ENSE00001450968 3
X 154409196 154409112 ENST00000014935 ENSE00001050508 2
X 154410039 154409418 ENST00000014935 ENSE00001050512 1
There is any way to get fasta sequence like this bed file. THanks in advance
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for loop command
written by harry •
Hello harry!
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Just get the fasta file with bedtools getfasta and then apply any of the solutions of that previous thread.
See below the command : There is for loop command in that I send you one which is bedtools get fasta command so in this, I used you reverse fasta command but it does not reverse at all, as you see I used reverse fast command in the pipe (|) so I thought it in continuation of previous commands then it give me reverse sequence but it didn't happen. So can I wrong anything?
seq=
bedtools getfasta -fi /Drive1/human_index/Homo_sapiens.GRCh38.dna.toplevel.fa -bed coords.bed -tab| bioawk -c fastx '{print ">"$name;print reverse($seq)}' |cut -f 2thanks in advance