Hi all,
I'm trying to learn how to analyze Chip-Seq data and the data file I'm using is the output from eland has the following format.
However, I'm trying to convert the eland output file into a six column table that can input into MACS algorithm for peak analysis
Chr Start End ?? tags sense
chr1. 233604 233639 0 2 -
I never processed Eland Result data before and am having a really hard time with reformating the original txt file. Therefore, any help will be appreciated!
Thanks!
•
written
by
Gavinupwht1996 •
1 answer
GenoMax poinst out ... ELAND ... what an old format, that brings up some memories
because the file format is so old it is unlikely that you'd find a tool to format it to your needs, you would need to write a program to reformat it, a program that is not particularly difficult to write, perhaps 20 lines of python code would do it,
- make an array as long as the chromosome
- set it all to zero
- as you go over the ELAND file increment the index of the array by one at index where the ELAND file matches
- that array will be your coverage, save it
a better solution would be to follow a tutorial that has a more modern data processing
Log in to answer this question.
-
Question about MACS2 genome size (other organism)
written by chansik •
-
Output from macs subcommand 'bdgpeakcall'
written by arsala521 •
-
Map-Reduce in Nextflow
written by russhh
-
HOMER annotatePeaks.pl 'Unique Peak ID' in first column changed in output file
written by theresa •
-
Selecting relevant binding sites according to MACS data
written by robbenstijn •
-
Data value in WIG file
written by Rishikesh Lotke •
-
Is it necessary to normalize sequencing data BEFORE input into MACS for ChIP-seq??
written by nash.claire
-
how to know the strands of MACS call peaks
written by catherine
-
Paired-end ChIP-Seq Peak Calling
written by simon.pearce •
-
Help With Understanding Macs Output. What Does Tags And Summit Exactly Mean?
written by Jordan
Do yourself a favor and find a recent dataset.
ELANDhas not been used for close to a decade.