search

cxzhu / Paired-seq

Paired-seq
14 stars 5 forks source link

Lacking source files of function bam2Mtx #3

Closed lfn17 closed 3 years ago

lfn17 commented 4 years ago

Hi Chenxu,

I notice the function of bam2Mtx in the reachtools package need a ref parameter (reachtools Bam2Mtx in.bam/in.sam [ref], ref is optional for RNA-seq but mandatory for ATAC-seq) However in the main.cpp, the ref parameter point to private files (such as mm10_1kb, does it mean a 1kb bed file for mm10 genome?) which are not available for custom users. Could you please provide a header in the instruction if you are convenient？ Thanks a lot!

Best, Fangnong

lfn17 commented 4 years ago

I notice the same question of issues 2, that is extremely helpful.

cxzhu commented 4 years ago

I notice the same question of issues 2, that is extremely helpful.

Hi Fangnong @lfn17

The ref files are required for both DNA and RNA, here the DNA ref are 1kb-binned file and RNA ref are ensemble genes. The header for the reference file should be:

DNA chrom pos_start pos_end bin_name_1 bin_name_2 chr1 0 1000 chr1:0-1000 chr1:0-1000 chr1 1000 2000 chr1:1000-2000 chr1:1000-2000

RNA chrom pos_start pos_end gene_ID gene_symbol chr1 3072253 3075322 ENSMUSG00000102693 4933401J01Rik chr1 3101016 3103125 ENSMUSG00000064842 Gm26206

I have added this header annotation into the source code to make it clearer to other readers. Thank you for your suggestion!

Best, Chenxu