Hi, I recently downloaded some solid short reads (35 bp), single end, and convert them in cfasta with ahi-dump.
I found that there are very few mappers that support solid read mapping in color space and finally i decided to use tophat using bowtie1 (which supported color space mapping).
Unfortunately I less less than 30 % of the reads mapping.
My previous experience has always been with 100 bp paired end reads, so I am not completely sure if I am using the right parameters for short read mapping:
tophat -G $annotation --segment-length 17 --segment-mismatches 1 -g 1 --bowtie1 -p 12 -o $OUTPUT_FOLDER --coverage-search --color --quals $genome $READ $QUAL
maybe is the segment-mismatch and maximum multi-hits too restrictive? (-g is 20 by default). What for your experience are the best parameters for short read mapping?
Thanks
Ilario
I found that there are very few mappers that support solid read mapping in color space and finally i decided to use tophat using bowtie1 (which supported color space mapping).
Unfortunately I less less than 30 % of the reads mapping.
My previous experience has always been with 100 bp paired end reads, so I am not completely sure if I am using the right parameters for short read mapping:
tophat -G $annotation --segment-length 17 --segment-mismatches 1 -g 1 --bowtie1 -p 12 -o $OUTPUT_FOLDER --coverage-search --color --quals $genome $READ $QUAL
maybe is the segment-mismatch and maximum multi-hits too restrictive? (-g is 20 by default). What for your experience are the best parameters for short read mapping?
Thanks
Ilario
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