Hi guys,
I'm totally new to NGS and have 2 fastq files corresponding to a paired-end illumina chipseq experiment. I am using bowtie to align the fastq : first i align only one fastq file then both of them. The % of reads with at least 1 reported alignment is so different for each case: 83% when i used only 1 fastq compared to ONLY 47% when i used both of them (as i should have). Anyone can explain me why ?
here are the results:
/bowtie -t -p 4 --sam --chunkmbs 1000 hg19/hg19 reads/V400can_chipseq_1.fastq > results/v400.sam
# reads processed: 15749589
# reads with at least one reported alignment: 13044920 (82.83%)
# reads that failed to align: 2704669 (17.17%)
Reported 13044920 alignments to 1 output stream(s)
Time searching: 00:32:23
AS OPPOSED TO:
./bowtie -t -p 4 --sam --chunkmbs 1000 -m 1 hg19/hg19 -1 reads/V400can_chipseq_1.fastq -2 reads/V400can_chipseq_2.fastq > results/v400_paired.sam
# reads processed: 15749589
# reads with at least one reported alignment: 7813517 (49.61%)
# reads that failed to align: 7480588 (47.50%)
# reads with alignments suppressed due to -m: 455484 (2.89%)
Reported 7813517 paired-end alignments to 1 output stream(s)
Time searching: 01:44:03
Thanks a mil in advance,
NZ
I'm totally new to NGS and have 2 fastq files corresponding to a paired-end illumina chipseq experiment. I am using bowtie to align the fastq : first i align only one fastq file then both of them. The % of reads with at least 1 reported alignment is so different for each case: 83% when i used only 1 fastq compared to ONLY 47% when i used both of them (as i should have). Anyone can explain me why ?
here are the results:
/bowtie -t -p 4 --sam --chunkmbs 1000 hg19/hg19 reads/V400can_chipseq_1.fastq > results/v400.sam
# reads processed: 15749589
# reads with at least one reported alignment: 13044920 (82.83%)
# reads that failed to align: 2704669 (17.17%)
Reported 13044920 alignments to 1 output stream(s)
Time searching: 00:32:23
AS OPPOSED TO:
./bowtie -t -p 4 --sam --chunkmbs 1000 -m 1 hg19/hg19 -1 reads/V400can_chipseq_1.fastq -2 reads/V400can_chipseq_2.fastq > results/v400_paired.sam
# reads processed: 15749589
# reads with at least one reported alignment: 7813517 (49.61%)
# reads that failed to align: 7480588 (47.50%)
# reads with alignments suppressed due to -m: 455484 (2.89%)
Reported 7813517 paired-end alignments to 1 output stream(s)
Time searching: 01:44:03
Thanks a mil in advance,
NZ
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