I am trying to map 10 million pairs of reads to the genome + splice junction templates. However Bowtie will not align most of the reads.
here is the command I used and the screen output (partial):
if I align them as single reads, majority reads are aligned:
I figured that it may be caused by the introns between the pair. what options I can use to make it work?
here is the command I used and the screen output (partial):
Code:
time bowtie -p 2 -v 2 -k 11 -m 10 -t --strata --best hg19.index -1 sample_10M_1.fastq -2 sample_10M_2.fastq sample.bowtie_aln.txt # reads processed: 9999641 # reads with at least one reported alignment: 317813 (3.18%) # reads that failed to align: 9679936 (96.80%) # reads with alignments suppressed due to -m: 1892 (0.02%)
Code:
bowtie -p 2 -v 2 -k 11 -m 10 -t --strata --best hg19.index -q sample_10M_1.fastq,sample$}_10M_2.fastq samplebowtie_aln_single.txt # reads processed: 19999282 # reads with at least one reported alignment: 16697210 (83.49%) # reads that failed to align: 3220837 (16.10%) # reads with alignments suppressed due to -m: 81235 (0.41%)
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