BS Mapping Oly Cats
Working on the genetics / epigenetics paper, I decided to try to concatenate all reads and align with Bismark in order to get some basic stats.
Here is the script.
tldr
#SBATCH --workdir=/gscratch/scrubbed/sr320/0620
${bismark_dir}/bismark \
--path_to_bowtie ${bowtie2_dir} \
-genome /gscratch/srlab/sr320/data/olurida-genomes/v081 \
-p 14 \
--non_directional \
/gscratch/scrubbed/sr320/0620/zr1394_all_s456_trimmed.fq
Final Alignment report
======================
Sequences analysed in total: 1635584275
Number of alignments with a unique best hit from the different alignments: 507562199
Mapping efficiency: 31.0%
Sequences with no alignments under any condition: 477689355
Sequences did not map uniquely: 650332721
Sequences which were discarded because genomic sequence could not be extracted: 496024
Written on June 30, 2019