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.
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.
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