Question: what is the cases when the insert size between mate pairs is zero?
0
gravatar for Medhat
3.4 years ago by
Medhat7.5k
Poland
Medhat7.5k wrote:

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

 

Thanks

sequence next-gen alignment • 904 views
ADD COMMENTlink modified 9 months ago by Biostar ♦♦ 20 • written 3.4 years ago by Medhat7.5k
1
gravatar for geek_y
3.4 years ago by
geek_y8.5k
geek_y8.5k wrote:

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

ADD COMMENTlink modified 9 months ago • written 3.4 years ago by geek_y8.5k

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/

ADD REPLYlink written 2.9 years ago by Biomonika (Noolean)3.0k

Wow. This looks great. Thanks.

ADD REPLYlink written 2.9 years ago by geek_y8.5k

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?

 

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by Medhat7.5k

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

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by Biomonika (Noolean)3.0k
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