Hello,
I have had a problem with mapping short reads generated from Illumina HiSeq to the assembly generated from velvet. I went through other threads not to post repeated questions but they did not solve my problem.
Basically, it give me very low mapping rates. Also, when I only used one pair of reads, it gave me higher mapping rate which is still low though. Does this mean I used a wrong script to split interleaved reads into separate R1 and R2 reads? Any suggestion would be appreciated.
1. When R1&R2 are used.
<Command>
bowtie index -q -1 R1.fastq -2 R2.fastq output
<Output>
# reads processed: 1705514
# reads with at least one reported alignment: 31904 (1.87%)
# reads that failed to align: 1673610 (98.13%)
Reported 31904 paired-end alignments to 1 output stream(s)
2. When only R1 used.
<Command>
bowtie index -q R1.fastq output
<Output>
# reads processed: 1705514
# reads with at least one reported alignment: 291167 (17.07%)
# reads that failed to align: 1414347 (82.93%)
Reported 291167 alignments to 1 output stream(s)
I have had a problem with mapping short reads generated from Illumina HiSeq to the assembly generated from velvet. I went through other threads not to post repeated questions but they did not solve my problem.
Basically, it give me very low mapping rates. Also, when I only used one pair of reads, it gave me higher mapping rate which is still low though. Does this mean I used a wrong script to split interleaved reads into separate R1 and R2 reads? Any suggestion would be appreciated.
1. When R1&R2 are used.
<Command>
bowtie index -q -1 R1.fastq -2 R2.fastq output
<Output>
# reads processed: 1705514
# reads with at least one reported alignment: 31904 (1.87%)
# reads that failed to align: 1673610 (98.13%)
Reported 31904 paired-end alignments to 1 output stream(s)
2. When only R1 used.
<Command>
bowtie index -q R1.fastq output
<Output>
# reads processed: 1705514
# reads with at least one reported alignment: 291167 (17.07%)
# reads that failed to align: 1414347 (82.93%)
Reported 291167 alignments to 1 output stream(s)
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