Can't tell the file format
Hi,
Can anyone help with a description of this file format? Obviously, it is neither fasta not fastq. It contains human RNA sequences.
hsa-miR-3670 AGAGCUCACAGCUGUCCUUCUCUA hsa-mir-3670-1 40
hsa-miR-548z CAAAAACCGCAAUUACUUUUGCA hsa-mir-548z 54
hsa-miR-28-5p AAGGAGCUCACAGUCUAUUGAG hsa-mir-28 14
hsa-miR-28-3p CACUAGAUUGUGAGCUCCUGGA hsa-mir-28 54
hsa-miR-3119 UGGCUUUUAACUUUGAUGGC hsa-mir-3119-2 9
hsa-miR-4314 CUCUGGGAAAUGGGACAG hsa-mir-4314 11
hsa-miR-4741 CGGGCUGUCCGGAGGGGUCGGCU hsa-mir-4741 59
Also, is it possible to convert a fasta file to this format?
Thanks!
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Gabe Anderson •
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Gabe Anderson •
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Did you ever find an answer to this?
To add to the original poster's question:
The software miRExpress requires a file for mature known miRNA sequences that is formatted like the above. The first three columns are pretty straight-forward, but it's not clear what the 4th column is supposed to be.
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ehscholl •
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Just tell us what you want to convert to what if that's what you need. This may not be any format in particular.
It looks just like a plain whitespace (tab ?)-delimited text file.
It's the pwt?dt format, of course!
I'm sorry I didn't get the format you mentioned. which is it, pls?
I was making a joke by abbreviating Jean-Karim's response. Your data is white space separated, and unless you give us more details on the tool that output it, we cannot help you with it.
I cant tell the tool that out put that data. I am trying to run miRExpress and one of their sample files come in that format. I tried both fa and fq and it returned a segmentation fault. So I am looking to convert my fa or fq file to this format to avoid the seg fault.
I believe that unless you provide as piece of that fasta file and desired output file for the same file, no one here can really help you.