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Forum: General

12-02-2017, 02:28 PM

Replies: 1

ChIP-Seq Intensity Analysis

Views: 1,494

Posted By __sequence

I'd say, you can calculate the coverage for all...

I'd say, you can calculate the coverage for all other proteins into BedGraph or BigWig files, and then intersect your BED file with the peaks of the first protein with the coverage files of other...

Forum: Bioinformatics

12-02-2017, 02:20 PM

Replies: 0

MACS2 output on Galaxy not readbale by BedTools on Galaxy

Views: 1,133

Posted By __sequence

MACS2 output on Galaxy not readbale by BedTools on Galaxy

Hi!

I am getting the following error with Galaxy (need to get an answer specifically for Galaxy; without Galaxy I am not getting this error):

I am running MACS2.1.0 in galaxy to determine...

Forum: Bioinformatics

11-25-2017, 04:20 AM

Replies: 2

Algebraic operations with genomic occupancy data

Views: 2,269

Posted By __sequence

Thank you! Is there also a software that allows...

Thank you! Is there also a software that allows to perform such operations with BedGraph files?

Forum: Bioinformatics

11-24-2017, 06:32 PM

Replies: 2

Algebraic operations with genomic occupancy data

Views: 2,269

Posted By __sequence

Algebraic operations with genomic occupancy data

Hi all,

What is a proper software to calculate the average between several genomic coverage signals (e.g. several ChIP-seq replicates, with single base-pair resolution)?

Thanks!

Forum: Bioinformatics

10-17-2017, 01:18 PM

Replies: 1

Print selected columns from a text file

Views: 960

Posted By __sequence

Print selected columns from a text file

[I have already found the answer, see below]

Hi all,

I am looking for a simple oneliner (preferably) to print only selected columns (given by their column numbers) from a tab separated text...

Forum: Bioinformatics

10-17-2017, 01:02 PM

Replies: 1

Bisulfite sequencing question

Views: 1,137

Posted By __sequence

Bisulfite sequencing question

Hi all,

A (may be) stupid question about bisulfite sequencing: Do we in general expect CpGs to be equally methylated on both strands? For example, I am looking at the processed data from this GEO...

Forum: Bioinformatics

06-09-2011, 07:02 AM

Replies: 27

Eland-to-Bed algorithm

Views: 10,808

Posted By __sequence

I tried using as suggested at your manual,...

I tried using
as suggested at your manual, but it returns an empty file. May be my file is not in a standard Eland export format? I have been told that this is the output from Eland.

Here is...

Forum: Bioinformatics

06-09-2011, 04:39 AM

Replies: 27

Eland-to-Bed algorithm

Views: 10,808

Posted By __sequence

Oups, I just edited my post above. I figured out...

Oups, I just edited my post above. I figured out about the directory, but there is still an error:
Error: Line 1 has an invalid read:
Error: Mismatches is less than 0

Forum: Bioinformatics

06-09-2011, 04:03 AM

Replies: 27

Eland-to-Bed algorithm

Views: 10,808

Posted By __sequence

Hi apfejes, Thank you for your reply. I...

Hi apfejes,

Thank you for your reply. I tried the following format: java -jar conversion_util/ConvertToBed.jar -aligner eland -input "input_dir/name" -output "output_dir" -name "name" -noprepend...

Forum: Epigenetics

06-08-2011, 09:43 AM

Replies: 0

10 Mb signal-free region in mouse chromosomes

Views: 1,589

Posted By __sequence

10 Mb signal-free region in mouse chromosomes

Hi all,

I am doing chromatin Chip-Seq, which should in principle give a more or less homogeneous distribution of mapped reads along the genome (OK, there are small changes, which are the aim of...

Forum: Bioinformatics

06-08-2011, 08:00 AM

Replies: 27

Eland-to-Bed algorithm

Views: 10,808

Posted By __sequence

mgogol, Thank you for posting. I have tried this...

mgogol, Thank you for posting. I have tried this script, and it returns an empty file. May be the problem is that it requires an additional file as input?

I have all chromosomes in one input...

Forum: Bioinformatics

06-08-2011, 05:14 AM

Replies: 27

Eland-to-Bed algorithm

Views: 10,808

Posted By __sequence

apfejes, could you please tell, what is the last...

apfejes, could you please tell, what is the last downloadable version of your program, and what is an example of a command line to use it? I need to convert a single file (whole genome, not divided...

Forum: Illumina/Solexa

06-08-2011, 05:07 AM

Replies: 0

Eland to Bed

Views: 1,314

Posted By __sequence

Eland to Bed

Hello,

I am looking for a script to convert Eland export file to .Bed and an example of a command line to use it. Could you please advise?

Thank you.

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