Fastq-to-BAM

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not able to run the project

1

please write readme in proper sequentially manner

Shrutiagarwal1805

SAMTOOLS_NCPUS is Unused

1

Appears in dedup_sort_run_parallel.pbs but not in dedup_sort.sh.

DarioS

Alternate Contig Alignments and Mapping Quality Zero

12

The majority of reads (particularly over exons) in a region of chr17 appear to have MAPQ being zero.  Copying and pasting one of their sequences into UCSC BLAT, it...

DarioS

Reference Bundle is Stored on Deprecated CloudStor Service

1

> The complete set of Hg38 required files can be downloaded with the following commands to the base directory > `wget https://cloudstor.aarnet.edu.au/plus/s/CHeAuEsBkHalDvI/download -O Reference.tar.gz` CloudStor is shutting down at the...

DarioS

With the recent 100-day file deletion policy, it is no longer suitable to have the pipeline code stored in `/scratch/projectID/` folder.

DarioS

BWA Results Vary Based on Thread Number

2

[Threads Used Affects Results](https://github.com/PapenfussLab/gridss/issues/450) > OK, the root cause is that bwa 0.7.17-r1188 MAPQ scores are not stable w.r.t to number of threads used to run bwa. ``` [ds6924@gadi-login-06 ~]$...

DarioS

Replace scratch pathname with just nci-parallel

calizilla

It might be valuable to have a script to look for failed alignments and create a new input file based on those (unless you decide to change everything to one...

DarioS