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Old 09-10-2014, 08:44 AM   #1
kamilo889
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Default BWA mem trouble: paired reads have different names

Hi all... recently I've received my raw data for Exome Sequencing .. .how ever when I try to use BWA mem appear this error:

[mem_sam_pe] paired reads have different names: "MG00HS15:414:C59DDACXX:1:1109:1869:1993", "MG00HS15:414:C59DDACXX:1:1109:2293:1994"

If anyone had this issue in the past and know how to solve ... please let me know.

Thanks.
Camilo
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Old 09-10-2014, 08:45 AM   #2
kamilo889
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Additional I'am running this samples in Illumina ... using the sure select capture kit.
I've use this method before but now ... crash
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Old 09-10-2014, 08:56 AM   #3
Brian Bushnell
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It would help if you posted your command line and explained your pipeline. Generally, problems like this are caused by using upstream processing tools incorrectly such that pairing information is corrupted. The solution is to redo the upstream processing, starting with the raw reads, with pair-aware tools.
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Old 09-10-2014, 10:02 AM   #4
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Hi thanks for your reply. I'm performing the first step aligning the fastq files to the hg19... My code is the next

/.bwa men -M -p hg19.fasta file1.fastq file2.fastq > file.sam
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Old 09-10-2014, 10:10 AM   #5
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Where did you get the fastq files? It's likely that they're out of sync.
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Old 09-10-2014, 10:22 AM   #6
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Macrogen ....
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Old 09-10-2014, 10:26 AM   #7
dpryan
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And you didn't do anything to the files after downloading them? Then they likely f'd them up. You can follow instructions here or here to resync the files. This is assuming that they're paired-end and that they didn't just upload the dataset in multiple files, of course.
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Old 09-10-2014, 10:34 AM   #8
GenoMax
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Brian has a simple way to fix this problem in BBTools: http://seqanswers.com/forums/showpos...0&postcount=45
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Old 09-10-2014, 11:33 AM   #9
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Hi ... thanks again for your reply ... I didnt do nothing only download the data and un-gunzip it... I will read the posts that you recommend ...thanks again!
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Old 09-10-2014, 11:33 AM   #10
dpryan
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Quote:
Originally Posted by GenoMax View Post
Brian has a simple way to fix this problem in BBTools: http://seqanswers.com/forums/showpos...0&postcount=45
That's certainly more convenient than some obscenely long awk command!
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Old 09-10-2014, 11:34 AM   #11
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seems easy a lot!
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Old 09-10-2014, 11:55 AM   #12
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ajajaj well I have small issue runing bbmap ...

this is my input:
./repair.sh -Xmx8g in1=/Users/monicagiraldo/NGS/RawData/ISBA/H-ISBA_1.fastq in2=/Users/monicagiraldo/NGS/RawData/ISBA/H-ISBA_2.fastq out1=/Users/monicagiraldo/NGS/RawData/ISBA/Fixed/ISBA1fixed.fastq out2=/Users/monicagiraldo/NGS/RawData/ISBA/Fixed/ISBA2fixed.fastq outsingle=ISBAfixedsingle.fastq

but appear that this folder is missing or can't be charged:
Software.bbmap.current


thanks again .. sorry for botther
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Old 09-10-2014, 12:14 PM   #13
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Solved!!!!
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Old 09-10-2014, 01:49 PM   #14
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looking in the bwa documentation seems to be a problem when I use the -p option ... after run bbtools for paired data and remove the -p bwa runs properly
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Old 09-10-2014, 01:58 PM   #15
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Oh, I see the problem. Yes, the -p, I guess, made it try to use the first input file as if it was interleaved, which it wasn't. Looks like -p has different meaning for indexing and mapping, which is a little confusing.
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