B. Arman Aksoy

Confirm that use of BLAST's `-max_target_seqs` is intentional

1

Hi there, This is a semi-automated message from a fellow bioinformatician. Through a GitHub search, I found that the following source files make use of BLAST's `-max_target_seqs` parameter: - [dataAnalysis/RNA-Seq/annotating-transcripts.md](https://github.com/ISUgenomics/bioinformatics-workbook/blob/2210a7ebab4eb15d2ba40d24d3ed326a4d187f78/dataAnalysis/RNA-Seq/annotating-transcripts.md)...

Allow server/client speak gzip especially as part of the `Submit_targets` protocol

1

This is often not a big issue, but when you are sequentially submitting more than 10 complete epidisco workflows to a single server, sending them all do take some time....

Allow dumping/cleaning the job history via a ketrew subcommand

2

The pagination and filtering by job names using the web UI quickly becomes harder and harder as the number of (sometimes repetitive) job submissions get higher and higher. It would...

Hi there, This is a semi-automated message from a fellow bioinformatician. Through a GitHub search, I found that the following source files make use of BLAST's `-max_target_seqs` parameter: - [runBLASTn.sh](https://github.com/ISUgenomics/common_analyses/blob/3d57e6f489bbe652663fc90769ef5935c97b7934/runBLASTn.sh)...

Hi there, This is a semi-automated message from a fellow bioinformatician. Through a GitHub search, I found that the following source files make use of BLAST's `-max_target_seqs` parameter: - [blast_wrapper.sh](https://github.com/ISUgenomics/common_scripts/blob/3ff47b65cae0fe9d3019cdbb34ffd582521d7b43/blast_wrapper.sh)...

Make example data sets public

3

Here are the ones that we are familiar with and trust the most: ```bash $ gsutil ls gs://musc-codex/datasets/ \ | grep "20180706\|20180614" \ | xargs -I@ -P1 bash -c "gsutil...

Some preliminary notes: # Cytokit on gcloud Spin up a machine on gcloud: 2 GPUs Nvidia K80 ```bash gcloud beta compute \ --project=hammerlab-chs \ instances create \ cytokit \ --zone=us-east1-c...

Currently, the list is not that informative and needs more meat before being circulated.

This is just me thinking out loud while trying to re-run the pipeline for more than 80 patients to get the results from new type(s) of analyses/tools: I think we...

Things that can go wrong here include: - Mismatched sequencing platform - Sample mismatch/mix-up - ... And these can easily lead to some unexpected variant calling behavior (e.g. having tens...