Hi, everybody,
I am trying to use bwa mem (v. 0.7.12) on some interleaved fastq files, i.e. the reads are paired end, but they are in one file (the ith read is forward; ith+1 is the reverse).
after indexing the reference genome, I have used the command:
When I read the log file though, I get this:
[M:: bwa_idx_load_from_disk] read 0 ALT contigs
[M:: process] read 117486 sequences (10000027 bp)...
[M:: process] 117486 single-end sequences; 0 paired-end sequences
[M:: process] read 118316 sequences (10000081 bp)...
and so on. Does this mean bwa is not recognizing my reads as paired ends? Have I misunderstood the manual regarding the -p option?
Looking for advice
Thanks,
MAx
I am trying to use bwa mem (v. 0.7.12) on some interleaved fastq files, i.e. the reads are paired end, but they are in one file (the ith read is forward; ith+1 is the reverse).
after indexing the reference genome, I have used the command:
Code:
bwa mem -M my_ref.fa -p myfile.interleaved.fastq > ./mapped/my_file.sam
[M:: bwa_idx_load_from_disk] read 0 ALT contigs
[M:: process] read 117486 sequences (10000027 bp)...
[M:: process] 117486 single-end sequences; 0 paired-end sequences
[M:: process] read 118316 sequences (10000081 bp)...
and so on. Does this mean bwa is not recognizing my reads as paired ends? Have I misunderstood the manual regarding the -p option?
Looking for advice
Thanks,
MAx
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