paired reads have different names
Dear all I have downloaded fastq file and run BWA mem.
~/bwa/bwa/./bwa mem -t 24 \
-R '@RG\tID:s99\tSM:Ex99\tPL:Illumina\tPU:Hiseq2500' \
-M /home/hg19/hg19.fa \
gfan787_1.fastq.gz gfan787_2.fastq.gz >g.sam
After that I took this message:
paired reads have different names: "PRWES615:444:HYMK3DSXY:3:1131:6280:20415", "PRWES615:444:HYMK3DSXY:3:1131:12255:20400"
It should be appreciated if you could let me know how I can solve it. Best
• 1,424 views
•
link
updated
by
GenoMax
•
written
by
daffodil •
•
written
by
daffodil •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Invalid CIGAR after using bam clipOverlap
written by MboiTui •
-
Nextflow crash on AWS Batch with transition error
written by hkarakurt
-
slurm batch
written by bestone •
-
What is the major problem with this pipeline of SNPs analysis?
written by kgwkk2 •
-
BWA-mem not working with Snakemake + singularity
written by brunobsouzaa
-
Using shell command in Nextflow DSL=2 for BWA mem aligner
written by rohitsatyam102
-
MarkDuplicates showing error, not recognising SM tag present in bam Header
written by rohitsatyam102
-
I can't see my bam file on igv
written by manubiomed20 •
-
BWA MEM 0.7.12 Error : [gzread] <fd:4>: invalid distance code
written by gsr9999
-
Error with MuTect: SAM/BAM file SAMFileReader is malformed
written by eem0306 •
you're using the wrong FASTQ files or you preprocessed them without keeping the original order.
Based on this part of read name it looks like it it the same flowcell/lane so most likely the two data files were separately trimmed.
daffodil : You can use
repair.shfrom BBMap suite to re-sync your data files and remove singleton/orphan reads.