very low number of reads aligned in bowtie (colourspace)
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?
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