Question: Illumina paired end read header difference- SPAdes bwa run ERROR
0
gravatar for ranjeet_maurya
13 months ago by
New Delhi, IN
ranjeet_maurya0 wrote:

At the time of "Mismatch correction" in SPAdesv3.10 Running bwa mem using bwa-spades , SPAdes pipeline abrupt abnormally with showing an error


ERROR:

[mem_sam_pe] **paired reads have different names**: "HWI-D00111:192:C39DEACXX:3:2101:13339503", "HWI-D00111:192:C39DEACXX:3:1901:13339503"
[mem_sam_pe] **paired reads have different names**: "HWI-D00111:192:C39DEACXX:3:2101:13339506", "HWI-D00111:192:C39DEACXX:3:1901:13339506"

Having illumina PE reads with headers

read_1
@HWI-D00111:192:C39DEACXX:3:**2101**:13339500 1:N:0:CGTACTAG
read_2
@HWI-D00111:192:C39DEACXX:3:**1901**:13339500 2:N:0:CGTACTAG

If i am n't wrong there is a difference in tile co-ordinates among two PE reads in FASTQ format(i do not have SRA file). So, what should i do with these reads to get my assembly completed?

ADD COMMENTlink modified 13 months ago by genomax57k • written 13 months ago by ranjeet_maurya0

download bbmap and use repair.sh from it like so:

./repair.sh in1=pair1.fastq in2=pair2.fastq out1=out_pair1.fastq out2=out_pair2.fastq outsingle=out_single.fastq

ADD REPLYlink written 13 months ago by stolarek.ir550

thanks stolarek.ir ..

ADD REPLYlink written 13 months ago by ranjeet_maurya0

It appears that the pairing of reads in your files is messed up. This happens if you trim your paired-end data files individually (rather than together using a paired-end aware data trimming program). You should ideally go back to original data and redo the trimming with both R1/R2 files in the same operation followed by alignments. Otherwise starting with the fastq files and "re-pairing" then as shown by @stolarker.ir is another option.

ADD REPLYlink modified 13 months ago • written 13 months ago by genomax57k

thanks genomax

ADD REPLYlink written 13 months ago by ranjeet_maurya0
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