what is the cases when the insert size between mate pairs is zero?

Question

[Medhat]

As the question indicates I would like to know what is the cases where the insert size between mate pairs is zero.

Thanks

Answer 1

[GouthamAtla]

If the mate pair fragment contains the junction adapter on both the mates it can be considered as true mate pair fragment. If the junction adapter is not present on both the mates or one of the mate, then that mate pair fragment is a normal DNA fragment and the fragment length might be less than the 2*read_length.

Or

One of the mate is not mapped or mapped to a different scaffold etc.

More info on how to asses mate-pair library quality: http://www.illumina.com/documents/products/technotes/technote_nextera_matepair_data_processing.pdf

[Biomonika (Noolean)]

I tried to describe important parts of this document in section "Trimming MATE-PAIR reads" here: http://sites.psu.edu/biomonika/2015/07/03/trim-now-or-never-pe-and-mp-adaptor-removal/

[GouthamAtla]

Wow. This looks great. Thanks.

[Medhat]

In the sanity_check.sh script the input is one file for example;

sanity_check.sh ./forward_reads.fastq

and in this step R2=$(echo $R1 | sed 's/R1.fastq/R2.fastq/g') you make the other direction file name?

[Biomonika (Noolean)]

yes, my files are usually named something_R1.fastq and something_R2.fastq for forward and reverse reads, respectively. So I provide only the name of first file to the script and I derive the name of the second file by substituting R1.fastq for R2.fastq