Hi All:
I have got an csv file containing the coordinates of a bunch of introns. I convert the coordinates of introns into bed files using
$ awk -F '[,]' 'NR>=2{print $2, $3, $4,$5,".", $7}' OFS='\t' All_retained_intron.csv > All_retained_intron.bed
Then I used the recommendations from here to extract 5utr/3utr/cds from gtf files I have used for mapping and other anlysis.
However, when I do the intersect:
$ bedtools intersect -a GRCm38_genes_introns_bed6.bed -b All_retained_intron.bed > IR_in_intron.bed
I met a problem:
* WARNING: File GRCm38_genes_introns_bed6.bed has inconsistent naming convention for record: CHR_MG4180_PATCH 109649750 109650579 ENSMUST00000203001_intron 1 +
* WARNING: File GRCm38_genes_introns_bed6.bed has inconsistent naming convention for record: CHR_MG4180_PA TCH 109649750 109650579 ENSMUST00000203001_intron 1 +
Then I searched a while and from website, and changed my command into:
$ bedtools intersect -nonamecheck -u -s -a All_retained_intron.bed -b GRCm38_genes_intron_bed6.bed > IR_in_CDS.bed
This time there is no error or warning. But all the generated files are empty. Can you help me on what is going on in my process? Thank you very much.
