Chromosome name in FindPeaks // Help with Output

[Romeo1-1]

Hello, thank you for this package!

I encountered a problem during the FindPeaks part. In my bam file, my chromosomes don't have the "chr" prefix.

FindPeaks(output.file = "Sierra/P1832_peaks.txt",
          gtf.file = "genes.gtf",
          bamfile = "test.bam",
          junctions.file = "test_.bed",
          ncores = 20)

I managed to find a way around the problem by changing the names in my bam files using samtools & then re-indexing. This requires 2 extra step and I saw that there is a "chr_name" option. But I tried different combinations, like chr.names = c("1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","X","Y", "M") but got no luck.

Do you have any idea that could help me ? Thank you very much in advance,

Rémi

[Romeo1-1]

Hello,

Since I have already opened an issue, I will ask my question here.

To give some context, I am comparing 2 samples from the same patient, before and after treatment (at diagnosis/relapse). I was able to use the package and adapt the vignette to my own data.

I have a question about the "PlotCoverage" graph. Is there any way to tell exactly if a specific alternative transcript is present or not?

Here for example, I am very interested in the ENST000000424814 transcript (with spliced exon 10). But the peaks don't really allow to differentiate all these transcripts.

Thanks a lot in advance,

[rj-patrick]

Hi Romeo,

Regarding the first issue, the easiest thing if possible is to use the same GTF file that was used to generate the BAM file. Did you align the data yourself or did you acquire the BAM file as is?

Regarding the second issue, unfortunately Sierra does not have ability to evaluate specific transcripts. However, you might be able to check in IGV whether there are spliced reads skipping that exon of interest.

Cheers,
Ralph

[Romeo1-1]

Hello @reprobate , sorry for the late answer ! By using the exact same GTF file I got rid of the issue ! I was able to see alternative splicing on IGV but I hoped to be able to quantify one specific transcrit.

Thank you for your help,

Remi