I am trying to map Illumina GA II E paired end reads to a reference genome.
More than 80 % of the reads map when using single end mapping, but virtually none of the reads map when I am using paired end mapping.
Can some one please have a look at the commands I am using and a typical example of a read I have pasted below ? Any suggestions are welcome.
Thanks in advance
Adarsh Jose
BCB, Iowa State University
I am using the following commands:
# paired end
bowtie Ref/ZmB73_RefGenome -1 sample_s4_1.fastq -2 sample_s4_2.fastq s4PairedMapping.map -n 2 -e 250 -l 30 -I 400 -X 460 -m 10 --time --un Unmappedpaireds4 --max Multipaireds4 -S -p 4 --verbose
# single end
bowtie Ref/ZmB73_RefGenome sample_s4_1.fastq s4SingleMapping_1.map -e 250 -l 30 -m 10 --time --un Unmappedsingles4_1 --max Multisingles4_1 -p 4
bowtie Ref/ZmB73_RefGenome sample_s4_2.fastq s4SingleMapping_2.map -e 250 -l 30 -m 10 --time --un Unmappedsingles4_2 --max Multisingles4_2 -p 4
# An example mapping of a read pair
# Single end Pair1
ILLUMINA-4750D6_00031:4:1:10005:2856#0/1 + chromosome:AGPv2:2:1:237068873:1 32492480 CGGCGATATAAAATAAACAACTCAGAAGCAAATCGACCCCAGAAGCCCGTCTTAC ffafff]_dfac\\\cccfcccfcf]d^]b`b[`R`dbb`bcccad`J]`b^R]^ 0 2:A>G
# Single end Pair2
ILLUMINA-4750D6_00031:4:1:10005:2856#0/2 - chromosome:AGPv2:2:1:237068873:1 32492560 CCATGGCATCCGCTTCCTCCTCCCAGCAGAGAAGATTAGCCAGCTTGTAGTCCTTCTTCATAGGAGG ^]dbddd[Z^^[Z\U`^Icf[fehhhaefgh_ffdffd]_ffechehfccfa`X]^]T`]a\aaaad 0
#Paired End
ILLUMINA-4750D6_00031:4:1:10005:2856#0 141 * 0 0 * * 0 0 CCTCCTATGAAGAAGGACTACAAGCTGGCTAATCTTCTCTGCTGGGAGGAGGAAGCGGATGCCATGG daaaa\a]`T]^]X`afccfhehceff_]dffdff_hgfeahhhef[fcI^`U\Z[^^Z[dddbd]^ XM:i:0
ILLUMINA-4750D6_00031:4:1:10005:2856#0 77 * 0 0 * * 0 0 CGGCGATATAAAATAAACAACTCAGAAGCAAATCGACCCCAGAAGCCCGTCTTAC ffafff]_dfac\\\cccfcccfcf]d^]b`b[`R`dbb`bcccad`J]`b^R]^ XM:i:0
More than 80 % of the reads map when using single end mapping, but virtually none of the reads map when I am using paired end mapping.
Can some one please have a look at the commands I am using and a typical example of a read I have pasted below ? Any suggestions are welcome.
Thanks in advance
Adarsh Jose
BCB, Iowa State University
I am using the following commands:
# paired end
bowtie Ref/ZmB73_RefGenome -1 sample_s4_1.fastq -2 sample_s4_2.fastq s4PairedMapping.map -n 2 -e 250 -l 30 -I 400 -X 460 -m 10 --time --un Unmappedpaireds4 --max Multipaireds4 -S -p 4 --verbose
# single end
bowtie Ref/ZmB73_RefGenome sample_s4_1.fastq s4SingleMapping_1.map -e 250 -l 30 -m 10 --time --un Unmappedsingles4_1 --max Multisingles4_1 -p 4
bowtie Ref/ZmB73_RefGenome sample_s4_2.fastq s4SingleMapping_2.map -e 250 -l 30 -m 10 --time --un Unmappedsingles4_2 --max Multisingles4_2 -p 4
# An example mapping of a read pair
# Single end Pair1
ILLUMINA-4750D6_00031:4:1:10005:2856#0/1 + chromosome:AGPv2:2:1:237068873:1 32492480 CGGCGATATAAAATAAACAACTCAGAAGCAAATCGACCCCAGAAGCCCGTCTTAC ffafff]_dfac\\\cccfcccfcf]d^]b`b[`R`dbb`bcccad`J]`b^R]^ 0 2:A>G
# Single end Pair2
ILLUMINA-4750D6_00031:4:1:10005:2856#0/2 - chromosome:AGPv2:2:1:237068873:1 32492560 CCATGGCATCCGCTTCCTCCTCCCAGCAGAGAAGATTAGCCAGCTTGTAGTCCTTCTTCATAGGAGG ^]dbddd[Z^^[Z\U`^Icf[fehhhaefgh_ffdffd]_ffechehfccfa`X]^]T`]a\aaaad 0
#Paired End
ILLUMINA-4750D6_00031:4:1:10005:2856#0 141 * 0 0 * * 0 0 CCTCCTATGAAGAAGGACTACAAGCTGGCTAATCTTCTCTGCTGGGAGGAGGAAGCGGATGCCATGG daaaa\a]`T]^]X`afccfhehceff_]dffdff_hgfeahhhef[fcI^`U\Z[^^Z[dddbd]^ XM:i:0
ILLUMINA-4750D6_00031:4:1:10005:2856#0 77 * 0 0 * * 0 0 CGGCGATATAAAATAAACAACTCAGAAGCAAATCGACCCCAGAAGCCCGTCTTAC ffafff]_dfac\\\cccfcccfcf]d^]b`b[`R`dbb`bcccad`J]`b^R]^ XM:i:0
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