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Simon-Leonard / APERO

small RNA detection from paired-end RNA-seq data
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Error in `$<-.data.frame` #10

Closed mgsrod closed 1 year ago

mgsrod commented 1 year ago

Hi, I receive the following error when I attempt to run APERO:

Start detection with window = 1Error in $<-.data.frame(*tmp*, "ws", value = 0) : replacement has 1 row, data has 0 In addition: Warning message: In max(which(let < le[i])) : no non-missing arguments to max; returning -Inf

My input is as follows:b. APERO_start_detection(work_dir = ("/apero"), bam_name = "sortedbam.bam", ptt_file = NULL, wmax = 10, min_dist = 10, enrichment = 0.1, min_read_number = 0, genome_size = 2000000)

APERO is working with the sample data using the same options.

My BAM file is sorted and seems complete: @HD VN:1.0 SO:coordinate @SQ SN:KQ033870.1 LN:107658 @SQ SN:KQ033871.1 LN:2001565 @SQ SN:KQ033872.1 LN:3680 @SQ SN:KQ033873.1 LN:1903 @SQ SN:KQ033874.1 LN:1484 @SQ SN:KQ033875.1 LN:1478 @SQ SN:KQ033876.1 LN:610 @PG ID:bowtie2 PN:bowtie2 VN:2.2.5

Any ideas on how to fix this issue?

All the best,

Rod

Simon-Leonard commented 1 year ago

Hi Rod,

Is your data single end ?

Best, Simon

mgsrod commented 1 year ago

Hi Simon, Thanks for getting back to me so soon. Yes, its single end data.

mgsrod commented 1 year ago

Hi Simon,

Yes, it’s single end data

Rod Eyles, PhD Post Doctoral Researcher, Microbial Genomics & Symbiosis Lab @.***

Instituto Gulbenkian de Ciência Rua da Quinta Grande 6 2780-156 Oeiras, Portugal Website https://gulbenkian.pt/ciencia/ | Facebook https://www.facebook.com/InstitutoGulbenkianCiencia |  Instagram  https://www.instagram.com/igciencia/?hl=en | Twitter https://twitter.com/igciencia | LinkedIn https://www.linkedin.com/company/instituto-gulbenkian-de-ciencia/

On 6 Feb 2023, at 12:11 pm, Simon-Leonard @.***> wrote:

Hi Rod,

Is your data single end ?

Best, Simon

— Reply to this email directly, view it on GitHub https://github.com/Simon-Leonard/APERO/issues/10#issuecomment-1418982835, or unsubscribe https://github.com/notifications/unsubscribe-auth/A4THXWLML5FXDQOHBKTPQ2TWWDS6XANCNFSM6AAAAAAUSSEOKA. You are receiving this because you authored the thread.

Simon-Leonard commented 1 year ago

Initially APERO was not dedicated to work on single end data but I had some requests so I created a separated branch in github. Can you try the procedure mentionned in https://github.com/Simon-Leonard/APERO/issues/3#issuecomment-605458633 ? You just have to install a particular branch and add a parameter to the functions.

Simon