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fallerlab / ARF

Differential Ribosomal heterogeneity Prediction through Ribosome Profiling generated rRNA fragments and their Proximity to Ribosomal Proteins
GNU General Public License v3.0
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Does it matter which aligner I am using? #7

Closed ashakru closed 7 months ago

ashakru commented 8 months ago

Hi, thanks for developing such an interesting tool! It was great to see your poster during the Ribosome Heterogeneity meeting at the Royal Society!

I would like to give dripARF a go but I'm wondering whether there any preference regarding the aligner? I noticed that in the paper TopHat was used with the following parameters -n 2 --no-novel-juncs --no-novel-indels --no-coverage-search --segment-length 25. Sadly, TopHat is quite slow and with a large dataset I have, it will be painful to run. Do you have any experience with other aligners (eg. HISAT)? Any particular tags in BAM needed?

ferhatalkan commented 8 months ago

Hello Joanna, thank you for your interest in our tool. For the alignments, you can choose any aligner as long as you align to the right rRNA sequences and disable junctions and indels. Another thing is running dripARF with bam files is quite inefficient, so, I suggest using bedtools genomecov to create bedGraph files after the alignment step, for summarizing the read coverages on rRNAs.

ashakru commented 8 months ago

Amazing, that's super helpful. Many thanks for quick reply!