search

cxzhu / Paired-Tag

Analysis of Paired-Tag datasets
MIT License
39 stars 15 forks source link

Segmentation fault when converte rna bam to cell-counts matrice #10

Closed StrangerZN closed 2 years ago

StrangerZN commented 2 years ago

Segmentation fault when run "reachtools bam2Mtx2 ${s}_sorted_rmdup.bam ${mm10_rna}". I added "chr" prefix to the "./refereces/mm10.RNA.txt" and used it as the annotation file ${mm10_rna} here. mm10.fa downloaded from ucsc was used for earlier mapping.

Xieeeee commented 2 years ago

Hi, I think this is probably the issue with the mm10.RNA.txt annotation. The file is actually a four-columns file separated by tab, the last column is separated by space (e.g. ENSMUSG00000051951 Xkr4)

Would you mind telling us how you add the "chr" prefix? You can also try this and use the new annotation file. It should work: awk '{print "chr"$0}' ./refereces/mm10.RNA.txt > ./refereces/mm10.RNA.new.txt

Best, Yang

StrangerZN commented 2 years ago

Thanks! It works. I shouldn't replace the space in last column with tab.