search

sjroth / ARTDeco

MIT License
15 stars 7 forks source link

Inferring experiment type #2

Closed maxchang closed 5 years ago

maxchang commented 5 years ago

Had trouble running the preprocess command with a (matched) flu-infected RNA-seq experiment:

GTF file exists...
Gene annotation files exist...
Inferring BAM file formats...
Error... One or more files do not match in inferred format... Exiting...
BAM file ./A549_Mock_1.bam inferred as Paired-End, Strand-specific, and Forward-strand oriented...
BAM file ./A549_Mock_2.bam inferred as Paired-End, Strand-specific, and Forward-strand oriented...
BAM file ./A549_Flu_1.bam inferred as Paired-End and Single-stranded...
BAM file ./A549_Flu_2.bam inferred as Paired-End and Single-stranded...

I'm not sure how the experiment types are determined, but allowing the user to specify/override the automatic assignment would be helpful.

sjroth commented 5 years ago

Good idea will implement ASAP.

sjroth commented 5 years ago

Type assignment can now be specified by user. -layout -- options are PE or SE -stranded -- options are True or False -orientation --options are Forward or Reverse More details to come in next version/readme

sjroth commented 3 years ago

As written in the README, ARTDeco can only run on batches of files that have the same format. This is because different formats are processed differently by Homer and for consistency as batch effects can ruin output interpretation.

On Wed, May 26, 2021 at 1:04 AM Paulo Caldas @.***> wrote:

Quick question regarding this (already closed) issue: what was the source of the "error" above? is not possible to run ARTDeco with a mix of different file formats? i.e having a mix of bam files single- and paired-ended? I'm asking because I'm now trying that and it seems that I need to have the same format for all bam files

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/sjroth/ARTDeco/issues/2#issuecomment-848558808, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACEVD73OX25U37C2M2EHNS3TPSTRZANCNFSM4HJFWM2Q .

-- Samuel J Roth BA Biology, Computer Science, Wesleyan '13 MA Biology, Wesleyan '14 PhD candidate, Bioinformatics and Systems Biology, University of California, San Diego