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HuiyangYu / PanDepth

An ultra-fast and efficient genomic tool for coverage calculation
https://github.com/HuiyangYu/PanDepth
MIT License
137 stars 4 forks source link

Genome reference when running PanDepth #11

Open suminwei opened 3 weeks ago

suminwei commented 3 weeks ago

Hi, I was wondering if I would like to calculate coverage across the genome for specific window size (ex. 100kb) using a BAM file, do I need to supply a reference genome file when I run PathDepth? Or does the tool just use the alignment information contained in the BAM file? Thank you, Lisa

HuiyangYu commented 3 weeks ago

just bam!

---- Replied Message ---- | From | @.> | | Date | 11/07/2024 23:08 | | To | @.> | | Cc | @.***> | | Subject | [HuiyangYu/PanDepth] Genome reference when running PanDepth (Issue #11) |

Hi, I was wondering if I would like to calculate coverage across the genome for specific window size (ex. 100kb) using a BAM file, do I need to supply a reference genome file when I run PathDepth? Or does the tool just use the alignment information contained in the BAM file? Thank you, Lisa

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: @.***>

suminwei commented 3 weeks ago

Okay thank you!