Tavi Nathanson

Sounds like a reasonable thing to have 👍

:+1:

To summarize what we just talked about: - Truncation is happening here: https://github.com/hammerlab/cycledash/blob/master/cycledash/static/js/comments/components/comment.js#L71 - You suggested that truncation should probably happen on the thin comment feed, but not the all...

Hey @zhangyonglzg, this is RNA-Seq data processed with Kallisto to get transcript-level abundances per patient (you can see the Kallisto output files at http://doi.org/10.5281/zenodo.546110), and then processed with tximport (in...

Yup, that's right. For those using the provided Python code, that is addressed in https://github.com/hammerlab/multi-omic-urothelial-anti-pdl1/blob/master/analyses/utils/data.py#L453

Hi Guillaume, I don't believe the BAM files are publicly available yet, unfortunately. If you send me your email address, I can put you in touch with someone who can...

Hey @GuillaumeRS, thanks for checking in -- the raw data is very close to being available on dbGaP! We're keeping track of your request and I hope you'll be able...

Per https://github.com/hammerlab/biokepi/issues/419#issuecomment-280073430, it may not be worth it to add this with razerS3 vs. an aligner that won't require 208GB+ of memory (or no possible GCP machine type for high...

@armish and I agreed that the `razers3` pre-filtering step (vs. using a different aligner) doesn't seem particularly high priority, since (a) there's a good chance it wouldn't impact results (and...

When running `samtools index`: ``` [W::bam_hdr_read] EOF marker is absent. The input is probably truncated. samtools index: "/nfs-pool-2/biokepi/work/results-b37decoy-dna_processing_137/1b75bb82f758c48a9a243a123afc4b54_checkpoint-trials_lung_ipinivo_tumor_bams_AB653591-5_bamAB653591-5-sorted.bam" is corrupted or unsorted ``` From @armish: > definitely a truncated BAM...