Hi,
I need to process my miRNA fasta file to end up with a collapsed fasta (read count format).
I have used fastx_collapser for this task, that gives me the following output:
>1-327278
CGCGACCTCAGATCAGACGT
>2-226606
TATTGCACTTGTCCCGGCCTGT
>3-206069
GAAGCGGGTGCTCTTATTTT
....etc.
However, I would need this file to be formatted as follows:
CGCGACCTCAGATCAGACGT 327278
TATTGCACTTGTCCCGGCCTGT 226606
GAAGCGGGTGCTCTTATTTT 206069
....etc.
so its sequence, followed by a tab and read count number. I need this format, since I'm going to feed the file in a subsequent analysis program.
Is there any way to collapse a fasta file and get the output in a desired format?
Or maybe somebody could suggest a simple way of reformatting the fastx_collapser file?
I need to process my miRNA fasta file to end up with a collapsed fasta (read count format).
I have used fastx_collapser for this task, that gives me the following output:
>1-327278
CGCGACCTCAGATCAGACGT
>2-226606
TATTGCACTTGTCCCGGCCTGT
>3-206069
GAAGCGGGTGCTCTTATTTT
....etc.
However, I would need this file to be formatted as follows:
CGCGACCTCAGATCAGACGT 327278
TATTGCACTTGTCCCGGCCTGT 226606
GAAGCGGGTGCTCTTATTTT 206069
....etc.
so its sequence, followed by a tab and read count number. I need this format, since I'm going to feed the file in a subsequent analysis program.
Is there any way to collapse a fasta file and get the output in a desired format?
Or maybe somebody could suggest a simple way of reformatting the fastx_collapser file?
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