Give different names to plus and minus strand when exporting to BedGraph

[Hami7407]

Hello, I am trying to export to the BedGraph File.

However, I only receive tag cluster file not divided into two strands.

This is what I did

> trk <- exportToTrack(CTSSnormalizedTpmGR(humanS_cluster, "Adult_brain_1S"))
> humanS_cluster |> CTSSnormalizedTpmGR("all") |> exportToTrack(humanS_cluster, oneTrack = FALSE)
GRangesList object of length 2:
[[1]]
UCSC track 'Adult_brain_1S (TC)'
UCSCData object with 1310873 ranges and 5 metadata columns:
            seqnames    ranges strand |    genes annotation filteredCTSSidx     score     itemRgb
               <Rle> <IRanges>  <Rle> |    <Rle>      <Rle>           <Rle> <numeric> <character>
        [1]     chr1    564451      + | MTND1P23   promoter            TRUE   3.05356       black
        [2]     chr1    564455      + | MTND1P23   promoter            TRUE   1.56056       black
        [3]     chr1    564456      + | MTND1P23   promoter            TRUE   3.05356       black
        [4]     chr1    564463      + | MTND1P23   promoter            TRUE   5.97491       black
        [5]     chr1    564560      + | MTND1P23   promoter            TRUE   1.56056       black
        ...      ...       ...    ... .      ...        ...             ...       ...         ...
  [1310869]     chr1 249211204      - |             unknown            TRUE   1.56056       black
  [1310870]     chr1 249212177      - |             unknown            TRUE   1.56056       black
  [1310871]     chr1 249220686      - |             unknown            TRUE   1.56056       black
  [1310872]     chr1 249221821      - |             unknown            TRUE   1.56056       black
  [1310873]     chr1 249239784      - |             unknown            TRUE   1.56056       black
  -------
  seqinfo: 298 sequences (2 circular) from hg19 genome
[[2]]
UCSC track 'Adult_brain_1S (TC)'
UCSCData object with 502786 ranges and 5 metadata columns:
           seqnames    ranges strand |    genes annotation filteredCTSSidx     score     itemRgb
              <Rle> <IRanges>  <Rle> |    <Rle>      <Rle>           <Rle> <numeric> <character>
       [1]     chr1     82726      + |             unknown            TRUE   3.68027       black
       [2]     chr1    535277      + |             unknown            TRUE   3.68027       black
       [3]     chr1    540765      + |             unknown            TRUE   3.68027       black
       [4]     chr1    564575      + | MTND1P23   promoter            TRUE   3.68027       black
       [5]     chr1    564587      + | MTND1P23   promoter            TRUE  11.45750       black
       ...      ...       ...    ... .      ...        ...             ...       ...         ...
  [502782]     chr1 249200594      - |             unknown            TRUE   3.68027       black
  [502783]     chr1 249200611      - |             unknown            TRUE   3.68027       black
  [502784]     chr1 249200695      - |             unknown            TRUE   3.68027       black
  [502785]     chr1 249200790      - |             unknown            TRUE   3.68027       black
  [502786]     chr1 249201330      - |             unknown            TRUE   3.68027       black
  -------
  seqinfo: 298 sequences (2 circular) from hg19 genome

> trk <- split(trk, strand(trk), drop = TRUE)
> rtracklayer::export.bedGraph(trk, "Adult_brain_1S")
BiocFileList of length 2

Same thing happens when I used rtracklayer::export.bedGraph(trk, "Adult_brain_1S.bedGraph")

How can I get a bedGraph file of two different strands?

Thank you

[charles-plessy]

Dear Hami,

in my hands, with the example data from the vignette, the command works properly and produces one file containing two tracks. However, the tracks have the same name; is that the cause of your problem?

Have a nice day,

-- Charles

[Hami7407]

hmm... I only can download CAGE Tag cluster file which are not divided into two strands even though I export the data after split them into two. When I open the file, it has only positive numbers.

I thought I don't have to specify which strand I want to download if I use export.bedGraph command. Could you help me with this? It was all working with the CAGEr previous version.

Thank you,

Best

[charles-plessy]

Can you try something like:

trkBG <- split(trk, strand(trk), drop = TRUE)
trkBG[['+']]@trackLine@name <- paste0(trkBG[['+']]@trackLine@name, " +")
trkBG[['-']]@trackLine@name <- paste0(trkBG[['-']]@trackLine@name, " -")
trkBG[['+']]@trackLine@description <- paste0(trkBG[['+']]@trackLine@description, ", + strand")
trkBG[['-']]@trackLine@description <- paste0(trkBG[['-']]@trackLine@description, ", - strand")
rtracklayer::export.bedGraph(trkBG, "myBedGraphTrack.bedGraph")

If it works I will correct the documentation and try to add a function for such strand splitting.

[Hami7407]

Thank you for the suggestion! However, it only gives me + strand... somehow I can't download minus strand

Sorry for the issues!

[charles-plessy]

Can you double-check that the minus-strand information is present in the data you send to the UCSC browser? On my computer, with CAGEr's example data I have:

$ grep track myBedGraphTrack.bedGraph 
track name="Zf.30p.dome (TC)+" description="Zf.30p.dome (CAGE Tag Clusters (TC))" visibility=full type=bedGraph
track name="Zf.30p.dome (TC)-" description="Zf.30p.dome (CAGE Tag Clusters (TC))" visibility=full type=bedGraph

Also, if I remember well the previous version of CAGEr was exporting the plus and minus strand in separate files. You can still do that too with something like:

rtracklayer::export.bedGraph(trkBG[['+']], "myBedGraphTrackPlus.bedGraph")
rtracklayer::export.bedGraph(trkBG[['-']], "myBedGraphTrackMinus.bedGraph")

[Hami7407]

trkBG <- split(trk, strand(trk), drop = TRUE) trkBG[['+']]@trackLine@name <- paste0(trkBG[['+']]@trackLine@name, " +") trkBG[['-']]@trackLine@name <- paste0(trkBG[['-']]@trackLine@name, " -") trkBG[['+']]@trackLine@description <- paste0(trkBG[['+']]@trackLine@description, ", + strand") trkBG[['-']]@trackLine@description <- paste0(trkBG[['-']]@trackLine@description, ", - strand") rtracklayer::export.bedGraph(trkBG, "myBedGraphTrack.bedGraph")

Sorry, I checked again with UCSC browser and minus strand exists! so the last code you gave me works!

Thank you