File format conversion

[harlock0083]

Hello,

I have a list of transcripts in a txt file that I would like to align my RNAseq data to. The file has the following tab-delimited format:

(column description)
1. Name of the interval
2. Chromosome
3. Strand
4. Interval start (with respect to the "+")
5. Interval end (with respect to the "+")
6. Number of sub-intervals
7. Sub-interval starts (with respect to the "+", comma-delimited)
8. Sub-interval end (with respect to the "+", comma-delimited)

Example from file:

REM2 chr14 + 22422271 22426729 5 22422271,22423722,22424314,22425072,22425662, 22422439,22424064,22424388,22425280,22426729,
SYNGR2 chr17 + 73676265 73680604 4 73676265,73678492,73679185,73679414, 73676391,73678730,73679325,73680604,

I was thinking to convert to a fasta file then using bowtie-build, but I haven't find the right tool to do the conversion. Any help would be appreciated.

[DZhang]

You need to write a script to process the file.

Best regards,
Douglas

https://www.contigexpress.com

[DFJ111]

Alternatively you could use Galaxy if you're not keen on writing scripts. Galaxy works quite well with tab-delimited files.

Either way, I'm assuming the coordinates refer to a DNA sequence file in some common format (Fasta)? You'd need to extract the relevant sequence from the fasta? file by reference to the coordinates. If you can get them into the last tab of the tab-delimited format, then you could just delete all the other tabs except for the 1st, then convert to fasta either by writing a script or in Galaxy.

[maubp]

That output looks a bit like BLAT output... what tool is your file from? Perhaps there is an existing parser you could use.