grenaud
commented
6 years ago Dear mmaitenat, thank you for submitting this, you are 100% right. Is seems that ART just writes 1 number if the read length for single and paired-end mode are the same. This is confusion but I changed it to:
(single-end, paired-end)
GA2 - GenomeAnalyzer II ( 50bp, 75bp)
HS20 - HiSeq 2000 ( 100bp, 100bp)
HS25 - HiSeq 2500 ( 125bp, 150bp) (Default)
HSXt - HiSeqX TruSeq ( 150bp, 150bp)
MSv1 - MiSeq v1 ( 250bp, 250bp)
MSv3 - MiSeq v3 ( 250bp, 250bp)
I this corrects the read length problem, let me know if I can close the issue.
mmaitenat
Hi! I've been using gargammel for a while and I think I encountered some issue with the available options for the sequencing system to be used to simulate the reads. When I look at the help of gargammel through
./gargammel.pl -h, I get the following as to the -ss option:-ss [system] Illumina platfrom to use, the parentheses indicate the max. read length use the shorthand in the left column: (single-end, paired-end) GA2 - GenomeAnalyzer II ( 50bp, 75bp) HS20 - HiSeq 2000 ( 100bp, N/A) HS25 - HiSeq 2500 ( 125bp, 150bp) (Default) HSXt - HiSeqX TruSeq ( 150bp, N/A) MSv1 - MiSeq v1 ( 250bp, N/A) MSv3 - MiSeq v3 ( 250bp, N/A)
According to this, only GA2 and HS25 can be used with paired-end reads. However, and correct me if I am wrong, when I check ART, which is the program used for creating the reads, I saw that the six of them can be used with paired-end reads. I also noticed that those length values between parentheses just correspond to lengths for which error profiles have been created.
Could you tell if I am missing something or this is actually some mistake here? Many thanks!!