search

JiekaiLab / scTE

MIT License
87 stars 27 forks source link

chromosome number must be consistent when using scTE ? #17

Open akui113 opened 3 years ago

akui113 commented 3 years ago

Hi Jiekai Lab, Very nice work ! one problem is that the chromosome number (1,2,3,4....., X, Y.) of the bam file must be consistent with the chromosome number (chr1,chr2.....,chrX,chrY) of the gene annotation file (hg38.exclusive.idx) ?

Actually, my bam files use chromosome numbers 1, 2, 3, 4...., X, Y. However, the genome annotations file (hg38.exclusive.idx) generated by scTE was numbered chr1, chr2..., chrX, chrY . Then, I tested my bam files and annotated with hg38.exclusive.idx and get the result, but I don’t know if the result obtained by this way is right?

Thank you very much.

Kui Duan

jphe commented 3 years ago

Hi Kui,

scTE will deal with the "chr" issue automatically, your output should be correct.

akui113 commented 3 years ago

@jphe wow! best software, thank you for your helping !