I'm using HTQC for a metagenomic pipeline, but I'm getting troubles when I use a fastq file over 200bp long (this is the test file I'm using: http://goo.gl/LInb3). More concretely, the program don't run and return a "segment violation" error. I've tried with shorter segments (100bp and 180bp) and it works fine.
I would like to know if there is some way to fix this error.
Thanks a lot.
Last edit: Arnau 2013-03-28
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Really sorry for not noticed your post for a pretty long time. I tried ht-stat using SRR513804, it seems version 0.14.1 now works.
By the way, SRR513804 is not a 200bp library. It's paired-end 100bp. When you dump them into FASTQ using NCBI's fastq-dump, you should use --split-files or --split-spot option to get the ends properly splitted.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi,
I'm using HTQC for a metagenomic pipeline, but I'm getting troubles when I use a fastq file over 200bp long (this is the test file I'm using: http://goo.gl/LInb3). More concretely, the program don't run and return a "segment violation" error. I've tried with shorter segments (100bp and 180bp) and it works fine.
I would like to know if there is some way to fix this error.
Thanks a lot.
Last edit: Arnau 2013-03-28
Really sorry for not noticed your post for a pretty long time. I tried ht-stat using SRR513804, it seems version 0.14.1 now works.
By the way, SRR513804 is not a 200bp library. It's paired-end 100bp. When you dump them into FASTQ using NCBI's fastq-dump, you should use --split-files or --split-spot option to get the ends properly splitted.