search

COMBINE-lab / oarfish

long read RNA-seq quantification
BSD 3-Clause "New" or "Revised" License
71 stars 3 forks source link

Inferential replicates and .pq file creation #34

Closed margaux-david closed 12 hours ago

margaux-david commented 1 month ago

Hello !

I am new to these kind of analyses and have been running oarfish (v.0.6.2) with the following parameters/options: --single-cell, --alignments, --model-coverage and --num-bootstraps. I wanted to generate the .pq file for follow-up analyses, but it does not get generated. I tried setting --num-bootstraps to 30 and to 100, but no .pq file was created. I also tried with and without specifying --threads but still no luck... Can you help me solve this issue?

Thank you so much!

Kind regards

rob-p commented 1 month ago

Hi @margaux-david,

Thanks for raising this issue. Right now, inferential replicates are only output in bulk RNA seq quantification mode. While it would certainly be possible to provide this information in single cell, I'm not aware of any tool that can actually take advantage of this information (i.e. full inferential replicates for single-cell analysis). I'm curious what your target analysis and proposed pipeline are.

Best, Rob

margaux-david commented 1 month ago

Hi 😊

Thank you for this quick reply. We wanted to use the oarfish output as input for EdgeR, using a ‘customized’ version of the catchSalmon function. The data will be pseudobulked for some of the analyses, so running oarfish without the ‘—single-cell’ option may be an option in this case?

Kind regards,

Margaux

From: Rob Patro @.> Sent: 14 October 2024 16:13 To: COMBINE-lab/oarfish @.> Cc: Margaux David @.>; Mention @.> Subject: Re: [COMBINE-lab/oarfish] Inferential replicates and .pq file creation (Issue #34)

Hi @margaux-davidhttps://github.com/margaux-david,

Thanks for raising this issue. Right now, inferential replicates are only output in bulk RNA seq quantification mode. While it would certainly be possible to provide this information in single cell, I'm not aware of any tool that can actually take advantage of this information (i.e. full inferential replicates for single-cell analysis). I'm curious what your target analysis and proposed pipeline are.

Best, Rob

— Reply to this email directly, view it on GitHubhttps://github.com/COMBINE-lab/oarfish/issues/34#issuecomment-2411391433, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BMDBVVJGMQGSEIKTBIMRNJTZ3PGQHAVCNFSM6AAAAABP47STH2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMJRGM4TCNBTGM. You are receiving this because you were mentioned.Message ID: @.**@.>> [ { @.": "http://schema.org", @.": "EmailMessage", "potentialAction": { @.": "ViewAction", "target": "https://github.com/COMBINE-lab/oarfish/issues/34#issuecomment-2411391433", "url": "https://github.com/COMBINE-lab/oarfish/issues/34#issuecomment-2411391433", "name": "View Issue" }, "description": "View this Issue on GitHub", "publisher": { @.": "Organization", "name": "GitHub", "url": "https://github.com" } } ]