SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 13 of 13
Search took 0.00 seconds.
Search: Posts Made By: __sequence
Forum: General 12-02-2017, 01:28 PM
Replies: 1
Views: 917
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, 01:20 PM
Replies: 0
Views: 478
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, 03:20 AM
Replies: 2
Views: 652
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, 05:32 PM
Replies: 2
Views: 652
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, 12:18 PM
Replies: 1
Views: 434
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, 12:02 PM
Replies: 1
Views: 424
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, 06:02 AM
Replies: 27
Views: 9,088
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, 03:39 AM
Replies: 27
Views: 9,088
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, 03:03 AM
Replies: 27
Views: 9,088
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, 08:43 AM
Replies: 0
Views: 992
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, 07:00 AM
Replies: 27
Views: 9,088
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, 04:14 AM
Replies: 27
Views: 9,088
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, 04:07 AM
Replies: 0
Views: 964
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.
Showing results 1 to 13 of 13

 


All times are GMT -8. The time now is 01:58 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO