Can you create a chromatin assay using multiple fragment files for a single sample? (Fragments by chromosome?) #1699
Unanswered
aburdencoding
asked this question in
Q&A
Replies: 0 comments
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
-
Hello Signac community,
I am relatively new to R and Signac and am stuck on a sample that seems to have a non-standard data structure. I am trying to analyze a public dataset where the authors used custom Python code for the early parts of their analysis. I would like to use Signac for my analysis, but their output file formats are missing components that signac seems to require, specifically, a single fragments file. For each sample, there seem to be both .bed.bgz and the associated .bed.bgz.tbi indexed files; HOWEVER, it is not a single file but rather separated by chromosomes and for each sample (see image attached). Alternatively, there is a filed with all peaks (all_peaks.bed) that I tried to use for the fragment file, but it is not indexed. Does anyone know if there is some way to combine these files to create a single readable element for Signac? Or alternatively, if there is a way to read all in for signac together, or to load and combine them so that the CreateChromatinAssay() function only receives one file/variable for the fragments requirement?
Thank you for any help/insight!
Beta Was this translation helpful? Give feedback.
All reactions