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MalteThodberg / CAGEfightR

Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor
GNU General Public License v3.0
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Error in bw_mapper(seqinfo = seqinfo, strand = strand, ...) : all(width(o) == 1) is not TRUE #11

Open zya226 opened 3 years ago

zya226 commented 3 years ago

Hi Malte,

When I ran quantifyCTSSs step, I got an error "Error in bw_mapper(seqinfo = seqinfo, strand = strand, ...) : all(width(o) == 1) is not TRUE". Not quite sure about this error. All my bw files were generated based on a custom hg19 genome. So I generated a custom Seqinfo file call Seq. Below is the command I uesd: CTSSs <- quantifyCTSSs(plusStrand=bw_plus_test,

The output of this command is:

Checking design... Checking supplied genome compatibility... Iterating over 1 genomic tiles in 5 samples using 10 worker(s)... Importing CTSSs from plus strand... Error in bw_mapper(seqinfo = seqinfo, strand = strand, ...) : all(width(o) == 1) is not TRUE

Could you please help me look at it?

Thanks, Yong

MalteThodberg commented 3 years ago

Dear Yong,

Exciting to see you are considering CAGEfightR for your analysis!

There could be some issues with the formatting of the BigWig-files: Did you try the new checkCTSSs() function for seeing if the BigWigs are properly formatted?

zya226 commented 3 years ago

Hi Malte,

Thank you for your response. An error was reported when I used checkCTSSs() function for my bw_plus and bw_minus files. 

          Attempting import of supplied filename...
          Error in checkCTSSs(object) : 
          CTSSs are not bp-wise: Each range should be exactly 1 bp wide!
          Note: You can use `convertGRanges2GPos` function to correct for this.

My bigwig files were generated from converting bam to bigwig format. I tried to generate the right files using 'convertGRanges2GPos'. But it did not work. Do you have any suggestion about how to convert bam to bigwig in suitable for CAGEfightR? Or how could i convert my current bw_plus/minus files to the right bigwig format?

Thanks

MalteThodberg commented 3 years ago

How did you try convertGRanges2GPos? You would have to go something like, import %>% convert %>% export.

CAGEfightR is mainly focused on downstream analysis of CTSSs obtained from other sources, but does currently have an experimental function convertBAM2BigWig function you could try.