I am working with ChIP-seq paired-end data where there is concern that one or more of the biological replicates may not be very good, but it is unknown which replicate may have a problem (I suspect there has to be at least one poor replicate in the data). The first part of my question is very simple: what do you recommend that I do to find this replicate to either toss it or fix it with some quality trimming on the ends?
For the moment, I tried using bowtie2 to trim 10 bp from the 5' and 3' ends of the reads in each of my samples just to see whether this fixes my problem. To define what I mean by "problem": basically, my final results (gene list) does not come out as I would expect it to come out (there are no genes of a certain type that I am looking for based on my biological intuition for what I should be seeing). When I run bowtie2 with the trimming options set, I do indeed get my .sam files okay, but my error file tells me:
(ERR): bowtie2-align died with signal 2 (INT)
20172305 reads; of these:
20172305 (100.00%) were paired; of these:
3064536 (15.19%) aligned concordantly 0 times
13699211 (67.91%) aligned concordantly exactly 1 time
3408558 (16.90%) aligned concordantly >1 times
----
3064536 pairs aligned concordantly 0 times; of these:
807633 (26.35%) aligned discordantly 1 time
----
2256903 pairs aligned 0 times concordantly or discordantly; of these:
4513806 mates make up the pairs; of these:
...
↧