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grace-ac / paper-pycno-sswd-2021-2022

Repository for data, analyses, code, and figures associated with the paper for Summer 2021 P. helianthoides SSWD work.
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Low alignment rates (2021 exp)? #1

Open sr320 opened 4 months ago

sr320 commented 4 months ago

I am seeing some samples that have quite low alignment rates

rates

Do you see the same thing?

grace-ac commented 4 months ago

yes, i'm not sure how to run multiqc on sam files, but i looked at the hisat output files and the following libraries had low alignment rates (ranging 10-24%)
34, 35, 36, 37, 38, 39, 40,

the remaining libraries were all roughly around 76-80% alignment, with libraries 75 and 78 having 46% and 63% respectively

EDIT: double checked percentages and our numbers are the same!

sr320 commented 4 months ago

Does not seem to be related to treatment

did these happen to be extracted as same batch?

grace-ac commented 4 months ago

yes, right about treatment. i'll check my extraction notes for extraction batch date!

grace-ac commented 4 months ago

it looks like for my summer 2021 samples i didn't make a note in an obvious place about what batch the samples were extracted in. i'll keep digging through my notes and spreadsheets.