Hello, I am new to Bowtie, so please pardon my naivety.
I have a reads file in the following format, which I suppose is the Eland format because this file has an "eland_result.txt" extension :
Example of one read record:
>HWI-EAS107_3:3:1:64:354 AAATAACTCTCCCCATTATTCTTGACCAACGTT U0 1 0 0 chr3.fa 89017297 R ..
When I run this reads file containing reads in the above format in Bowtie, I get the following output (error):
Time loading forward index: 00:00:12
Time loading mirror index: 00:00:13
Error: reads file does not look like a FASTQ file
Time for 1-mismatch full-index search: 00:00:00
Time searching: 00:00:25
Overall time: 00:00:25
Since I do not have the data in the FASTQ format, I don't think I have any other options.
Is there a way by which I can still use Bowtie with the file in the above format ?
I have a reads file in the following format, which I suppose is the Eland format because this file has an "eland_result.txt" extension :
Example of one read record:
>HWI-EAS107_3:3:1:64:354 AAATAACTCTCCCCATTATTCTTGACCAACGTT U0 1 0 0 chr3.fa 89017297 R ..
When I run this reads file containing reads in the above format in Bowtie, I get the following output (error):
Time loading forward index: 00:00:12
Time loading mirror index: 00:00:13
Error: reads file does not look like a FASTQ file
Time for 1-mismatch full-index search: 00:00:00
Time searching: 00:00:25
Overall time: 00:00:25
Since I do not have the data in the FASTQ format, I don't think I have any other options.
Is there a way by which I can still use Bowtie with the file in the above format ?
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