Bowtie Aligning failed 100%

[HeidiLee]

Hello,

I am trying to use bowtie to align sanger human DNA reads on hg19. The command line I have used is:
./bowtie -p 1 -m 20 --best --sam hg19 ../Task/Source/454reads_test.fastq ../Task/Source/454reads_test.sam
and I got the following report:
# reads processed: 84205
# reads with at least one reported alignment: 0 (0.00%)
# reads that failed to align: 84205 (100.00%)
No alignments

The sequences seem unusually long, 300-400bases.
And actually, I am not sure if I should use hg19 as prebuild index. There several indexes fir H. Sapian.

Could any one please help me with this alignment?

Thank you very much in advance.

Heidi

[HeidiLee]

I think I need to use BWA-SW for sequences with long lengths.
I am still learning :0)

[arolfe]

Bowtie2, Blat, and Blast are also a possibilities.

Whatever you choose, make sure you understand how it decides what to report. Bowtie was tuned for short reads, so it will not report matches if there are more than a few snps. It's also sensitive to where the snps fall in the read- snps at the 5' end are in the region it uses as an alignment seed and it can't handle more than 2 there.

Bowtie2 lets you specify the minimum score to report a match in terms of the query length, which scales much better with increasing read lengths.