Refreshing the Caligus

Updated: February 05

Trimmed reads again increased mapping efficiency

Mapping efficiency:	28.2%
Mapping efficiency:	27.9%
Mapping efficiency:	21.8%
Mapping efficiency:	21.5%


Seems ok.. now will “post-process”. Specifically

And check out 5x coverage tracks!


output directory:

Updated: February 03

Mapping efficiency did in fact almost double

Mapping efficiency:	15.9%
Mapping efficiency:	15.6%
Mapping efficiency:	11.6%
Mapping efficiency:	11.4%

Average methylation about 2%


Will now try trimmed reads

Updated: January 30

With very low mapping efficiency (~8)

I reran

with a few alignment tweaks

--non_directional \
--dovetail \

I expect the non_directional (presuming accurate) could double efficiency.


In an effort to back into lice, I tried rerunning bismark such that we could visualize with reasonable thresholds. job:

Unfortunately this is all that was created

[sr320@mox1 1219]$ ls
merged_CpG_evidence.cov_10x.bedgraph			     Sealice_F1_S20_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq  slurm-1580450.out
*merged_CpG_evidence.cov_5x.bedgraph			     Sealice_F2_S22_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq  slurm-1580615.out
Sealice_F1_S20_R1_001_trimmed.5bp_3prime.fq.gz_C_to_T.fastq  Sealice_F2_S22_R2_001_trimmed.5bp_3prime.fq.gz_G_to_A.fastq  slurm-1590565.out

Did see one issue

[FATAL ERROR]:	Number of bisulfite transformed reads are not equal between Read 1 (#226106788) and Read 2 (#225857063).
Possible causes: file truncation, or as a result of specifying read pairs that do not belong to each other?! Please re-specify file names! Exiting...

Going to run raw reads.

dc277e523adb9a09b0fe139432cc0fc3  Sealice_F1_S20_L001_R1_001.fastq.gz
2e42b2d6f9d2cf8d610001921426f416  Sealice_F1_S20_L001_R2_001.fastq.gz
deacebe41dc6826091571aebd235fe1a  Sealice_F1_S20_L002_R1_001.fastq.gz
d838e9fd5e14d2fb3d3629c9d4af2ddc  Sealice_F1_S20_L002_R2_001.fastq.gz
2acb16a5f192e42a9cc057ba962a9950  Sealice_F2_S22_L001_R1_001.fastq.gz
5812d8a1d8e0af717743612d88022fd0  Sealice_F2_S22_L001_R2_001.fastq.gz
6082314c6680524041b7b99a79f7e913  Sealice_F2_S22_L002_R1_001.fastq.gz
0c944326b09da6f7d2a186505b749022  Sealice_F2_S22_L002_R2_001.fastq.gz

Here is the new job script:

Written on February 7, 2020