Question

reformat eland_result.txt to MACS input file

0

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3.1 years ago

Gavinupwht1996 • 0

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.

Eland Result.txt

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!

format • 771 views

ADD COMMENT • link updated 3.1 years ago by Istvan Albert 100k • written 3.1 years ago by Gavinupwht1996 • 0

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Do yourself a favor and find a recent dataset. ELAND has not been used for close to a decade.

ADD REPLY • link 3.1 years ago by GenoMax 141k

score 1 · Accepted Answer · 2021-03-26

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