Tweet
Hello!
My first post, I couldn't find the answer by searching, so here goes:
Does anyone know if ENA submissions are required to include the fragment size of the reads? If a submission contained fragment size info, do you know where I might find it?
I checked the study, sample, and experiment XML files for the read data I'm interested in, and I found the read length listed, but not the fragment size. The reads are single-end, according to the experiment XML file.
Why I think I need this information:
I'm a grad student and our lab is completely new to NGS (my first Illumina run for a ChIP-seq experiment will be finishing up next week), and in the meantime I'm trying to familiarize myself with different peak callers. If I understand correctly, fragment size is an important parameter passed to callers (SICER for example) in order to correctly locate the center of the called peak by shifting the "read peak" by fragment size/2.
Absent any reported fragment size, and knowing that the ENA data is from a ChIP-seq experiment, is it reasonable to estimate a fragment size of between 150 and 200 bases for single-end Illumina reads?
My first post, I couldn't find the answer by searching, so here goes:
Does anyone know if ENA submissions are required to include the fragment size of the reads? If a submission contained fragment size info, do you know where I might find it?
I checked the study, sample, and experiment XML files for the read data I'm interested in, and I found the read length listed, but not the fragment size. The reads are single-end, according to the experiment XML file.
Why I think I need this information:
I'm a grad student and our lab is completely new to NGS (my first Illumina run for a ChIP-seq experiment will be finishing up next week), and in the meantime I'm trying to familiarize myself with different peak callers. If I understand correctly, fragment size is an important parameter passed to callers (SICER for example) in order to correctly locate the center of the called peak by shifting the "read peak" by fragment size/2.
Absent any reported fragment size, and knowing that the ENA data is from a ChIP-seq experiment, is it reasonable to estimate a fragment size of between 150 and 200 bases for single-end Illumina reads?