very low number of reads aligned in bowtie (colourspace)

Question

[Lila M]

Hi there, I would like to map a file with the human genome GRCh38. They used Solid technology to generate the file, so what I did was to generate the index as follow:

bowtie-build -C GRCh38.p10.genome.fa human_index_bowtie1/colour_index

and then run bowtie1

bowtie -p 8 -t -C human_index_bowtie1/colour_index SRR11557616.fastq.gz -S  SRR11557616.sam

however, I've got a very low number of reads mapped:

# reads processed: 37684092
# reads with at least one reported alignment: 2864697 (7.60%)
# reads that failed to align: 34819395 (92.40%)
Reported 2864697 alignments

The fastqc analysis was not terrible, and have some issues but I don't expect a better result if I do a trimming.

Any suggestion about how to improve the quality of the mapping? Thanks!!!

[GenoMax]

You should perhaps use BFAST (LINK) like the SRA entry notes. Not many aligners left that can deal with colorspace.

[Lila M]

Thank you! Is there any manual or more information about how to use it?

[GenoMax]

Program presumably should have in-line help or a doc file. Get the code and see what you find. Since SRA entry says they used this it should work (in theory).