SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 6 of 6
Search took 0.00 seconds.
Search: Posts Made By: mkareta
Forum: Bioinformatics 09-20-2017, 10:53 AM
Replies: 1
Views: 333
Posted By mkareta
I should also note that I have not found any...

I should also note that I have not found any hidden characters in my file using both

sed -n 'l' alignment_cmd.sh
cat -A alignment_cmd.sh
Forum: Bioinformatics 09-20-2017, 10:35 AM
Replies: 1
Views: 333
Posted By mkareta
Bowtie2 not giving the proper # reads when combining replicates

Hi Folks,

I was hoping that someone could shed some light on an issue that is driving me crazy. I am aligning some trimmed reads (from cutadapt 1.9.1, PE mode) using bowtie 2 v2.3.2. I aligned my...
Forum: Bioinformatics 06-28-2017, 01:41 PM
Replies: 0
Views: 282
Posted By mkareta
Macs2 Combining PE & SE

Hi Folks,

I am trying to use macs2 to call peaks then utilize idr2 to identify the final peak list. I have three biological replicates, 2 PE and 1 SE, and a target gene KO control which is SE....
Forum: Bioinformatics 05-18-2017, 01:45 PM
Replies: 6
Views: 369
Posted By mkareta
That's it nucacidhunter. After checking with the...

That's it nucacidhunter. After checking with the sequencing core I realized that they utilized a library prep kit which include poly-T end labeling. I'll trim that sequence and proceed as normal.
...
Forum: Bioinformatics 05-18-2017, 09:28 AM
Replies: 6
Views: 369
Posted By mkareta
Hi Geno, No I have not, I'm trying to get in...

Hi Geno,

No I have not, I'm trying to get in touch with them now.

Unfortunately this is common to all of the second reads (4 samples total). I guess my concern is do I trim the first 15 nt and...
Forum: Bioinformatics 05-18-2017, 09:11 AM
Replies: 6
Views: 369
Posted By mkareta
FastQC finds poly-A in second paired-end read for ChIP-seq sample

Hi,

I apologize if this has been covered but I can't find an answer for the issue that I am seeing with some paired-end Chip-seq data.

In all of my samples the second read shows poor quality...
Showing results 1 to 6 of 6

 


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


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO