DiscoSNP 2.2.0 paired end reads

Question

[tkitapci]

Hi,

In version 2.1.7 there was an -m option for paired end reads. In 2.2.0 I don't see this option. How can I tell the program that reads are paired ? I understand that paired read information is not required to run the discoSNP but this option will make it more convenient to run the program. If there is no such option I can interleave 2 read files in 1 file.

Thanks

Best Regards
T. Hamdi Kitapci

Answer 1

[pierre.peterlongo]

Hi,

All information about paired end reads and how to handle file of files is in the documentation.

Case4: I've two read sets each composed two read files: reads1_R1.fq.gz and reads1_R2.fq.gz; and reads2_R1.fq.gz and reads2_R2.fq.gz:

fof.txt:
fof_reads1.txt
fof_reads2.txt
fof_reads1.txt
reads1_R1.fq.gz
reads1_R2.fq.gz

fof_reads2.txt:
reads2_R1.fq.gz
reads2_R2.fq.gz

[tkitapci]

Thanks for the quick reply. If I understand correctly this means if I have 20 datasets with paired-end reads then I need to have 20 text files each having the names of the 2 files and then put the names of these 20 files in another file. This seems quite inconvenient. I think I will interleave the reads and have them in a single file. Putting two reads in the same file should generate the same output right?

Thanks

Best Regards
T. Hamdi Kitapci