Question: paired-end files with reads on different strand
gravatar for tina.khajeh
4.8 years ago by
Iran, Islamic Republic Of
tina.khajeh0 wrote:

I want to align reads in 2 different files using paired-end alignment with the help of bowtie. when I try to align it with bowtie1 it fails and a little portion of it just align to the reference genome. I aligned each file separately as a single read and when checked 2 SAM output files I saw that the flag values for entries in first file and second file are 0 for some entries and 16 for others,which I think means that some reads for each file were on the + starnd and others on - strand also when flag value for entry number N is 0 for first file it's corresponding flag value for N'th entry in second file is 16 . I want to know what should to do if i want to align it bowtie1? Is it true if I reverse all entries in first file and make all reads of first file on the same strand and do the same thing for second strand and then align it?

other question is that bowtie2 can map these two files, how can I be sure that mapping is true?

ADD COMMENTlink modified 4.8 years ago by swbarnes27.5k • written 4.8 years ago by tina.khajeh0
gravatar for swbarnes2
4.8 years ago by
United States
swbarnes27.5k wrote:

Don't reverse your reads, paired end reads are supposed to be on opposite strands.  Bowtie is smart enough to know this.  The first thing I'd try is changing the settings to tell it to expect a very large potential insert size between the reads; I think bowtie often refuses to report alignments if it thinks the reads are too far apart, and the default distance is very small.

ADD COMMENTlink written 4.8 years ago by swbarnes27.5k

Thanks, The problem solved :)

ADD REPLYlink written 4.8 years ago by tina.khajeh0

If your problem got solved, please accept the answer by clicking on the green tick, which only you could see below the answer. 

ADD REPLYlink modified 4.8 years ago • written 4.8 years ago by Deepak Tanwar4.0k
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