Closed shashwatsahay closed 6 months ago
Hi
Is it necessary to align the sequence twice? My files are quite large takes approx 8 hours for one run of bwa mem.
Can we skip the alignement step in Step 1.2 of https://github.com/fulcrumgenomics/fgbio/blob/main/docs/best-practice-consensus-pipeline.md and directly proceed to GroupReadsByUmi and start the downstreams Phase 2 steps.
Any insights into why the prealignment is necessary will be helpful
Yes it is required, do you have someone that can help you at your organization to help mentor you why? We're available for consulting too: https://www.fulcrumgenomics.com/
Hi
Is it necessary to align the sequence twice? My files are quite large takes approx 8 hours for one run of bwa mem.
Can we skip the alignement step in Step 1.2 of https://github.com/fulcrumgenomics/fgbio/blob/main/docs/best-practice-consensus-pipeline.md and directly proceed to GroupReadsByUmi and start the downstreams Phase 2 steps.
Any insights into why the prealignment is necessary will be helpful