Question: How To Over Come With Unequal File Size Of Fastq [Paired End Reads 100+100] During Bowtie2 Mapping
1
gravatar for Raghav
6.4 years ago by
Raghav100
Allahabad, India
Raghav100 wrote:

hello Every one,

I have got another serious problem, when I was running bowtie2 align for paired end reads I have got an error which are mentioned bellow:

[cdac@nbri bowtie2-2.1.0]$ ./bowtie2-align -x tair10ref -1 /storage/home/cdac/raghav/sratoolkit.2.3.2-4-centos_linux64/bin/LIBSG306_R1_filtered.fastq -2 /storage/home/cdac/raghav/sratoolkit.2.3.2-4-centos_linux64/bin/LIBSG306_R2_filtered.fastq -S input.sam

Error, fewer reads in file specified with -1 than in file specified with -2 terminate called after throwing an instance of 'int' Aborted.

my read1 fastq file is lesser in size as compair to read2, As per as I am getting here it is just because of unequal reads in in both fastq files.

But, what is best possible way to over come this problem???? is there any technique or syntax or tools which could help me out.

bowtie2 fastq mapping • 9.2k views
ADD COMMENTlink modified 5.6 years ago by Biostar ♦♦ 20 • written 6.4 years ago by Raghav100
1

Are these trimmed reads, wherein you trimmed the two fastq files separately? If so, just retrim the original fastq files with a trimmer that can deal properly with paired-end data. If these are fastq files from the sequencer, you might contact whomever sequenced the samples and see if you can redownload the data; presumably one of the files is corrupt or otherwise truncated. Those are the easiest solutions.

ADD REPLYlink written 6.4 years ago by Devon Ryan92k

Dear dpryan, actually i have got illumina sequenced data as fstq1 and fastq2 file and data provider has mentioned that they have filtered these files at 20 phred quality. I am new one in field of NGS data analysis, so I do not have much idea of technicality, like what did went wrong with data,

No, this not a trimmed data, is there any difference if if we trim fastq1, fastq2 file individually and trim both file together [how do we trim it together???]

ADD REPLYlink written 6.4 years ago by Raghav100
1

It sounds like the sequencing provider screwed things up. With paired-end data, one needs to trim or otherwise process both files at the same time. The reads in them are in the same order, so if you filter out a read from fastq1 but not fastq2, then all subsequent reads in the files will be out of sync. What they should have done is used a program that would filter/trim reads and write unpaired reads to a separate file. This is the way most trimmers work.

In this case, you're best off following the links provided by ashutoshmits. If you use this sequencing provider again, tell them not to do this next time, since they're just making more work for you.

ADD REPLYlink written 6.4 years ago by Devon Ryan92k

yes..... I trapped here as you said earlier and I tried it at my level best to over cum with such problem like to remove unique reads from either files [fq1 and fq2] and synchronize both reads properly which keep only paired reads data but at the end of day unable got any fruitful result. please help or suggest me if you have any idea to over cum such a problem, thank you

ADD REPLYlink written 6.4 years ago by Raghav100

What have you tried and what have the results been? If push comes to shove, you (or I, as a last resort) can write a simple bash/python/perl script to do this sort of thing.

ADD REPLYlink written 6.4 years ago by Devon Ryan92k

before going to write any script, I tried to find out some existing program and fortunately I have got a python script fastqCombinePairedEnd.py written by Eric Normandeau, which resole it perfectly and it is working properly I tried no. of combinations to find bug, at last it succeeded to resolve my problem. Thnq for guiding me.. :)

ADD REPLYlink written 6.4 years ago by Raghav100
1

Some related posts. There are many that deal with the same topic. So search thoroughly and you should be able to get something.

How to sort two mate pair (fastq) files so that the order of the identifiers is the same?

filtering paired end reads

ADD REPLYlink modified 6.4 years ago • written 6.4 years ago by Ashutosh Pandey11k

Thank you for providing such a fruit full link

ADD REPLYlink written 6.4 years ago by Raghav100
2
gravatar for Ashutosh Pandey
6.4 years ago by
Philadelphia
Ashutosh Pandey11k wrote:

This post does exactly what you want. See the answer from the user lh3 (Dr. Heng Li)

Combining the paired reads from Illumina run

ADD COMMENTlink modified 6.4 years ago • written 6.4 years ago by Ashutosh Pandey11k
1
gravatar for Ashutosh Pandey
6.4 years ago by
Philadelphia
Ashutosh Pandey11k wrote:

I use the following tool to trim my paired end reads. It takes care of the orphan reads.

https://code.google.com/p/ea-utils/wiki/FastqMcf

ADD COMMENTlink written 6.4 years ago by Ashutosh Pandey11k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1927 users visited in the last hour