Question: Bismark reads failing to align
0
gravatar for Anna S
4.3 years ago by
Anna S500
PSU
Anna S500 wrote:

Hello,

I'm using Bismark for the first time, and 99.99% of the reads are failing to align for my paired dataset of seq length 51 bp.  I have tried using the default -l, as well as -l of 40, the default -n as well as -n of 1, the original fastq files as well as quality trimmed and adaptor cut ones, etc., but none of these variations have made much of a difference. The FastQC output shows that the per base and per sequence quality scores are very good. Do you have any suggestions on how to proceed?

Thank you!!

Anna

fastqc bismark • 1.3k views
ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by Anna S500
1
gravatar for dariober
4.3 years ago by
dariober9.5k
Glasgow - UK
dariober9.5k wrote:

Without more detail is hard to tell where the problem is... Assuming the reference genome is the correct one, I would try to align only read 1 and see if the mapping goes up. Also make sure the paired reads have been trimmed in such way that the two fastq files in a pair remain in sync (i.e. by using trim_galore)

ADD COMMENTlink written 4.3 years ago by dariober9.5k
0
gravatar for Anna S
4.3 years ago by
Anna S500
PSU
Anna S500 wrote:

Please delete this question as it turns out to have been my misunderstanding of the datasets (2 lanes of the same end files vs paired-end files).  Bismark is working great now!!

ADD COMMENTlink written 4.3 years ago by Anna S500
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