Entering edit mode
9.0 years ago
mgadrianam
▴
30
Hi, everyone
I want to know the count of reads that overlap, this is the bed file, when I used IGV I found that in position for example, 51693268-51693291 of microRNA-125 on differents bams file have 12, 73, 75, 379, 400
chr19 10552122 10552144 hsa-miR-1238-5p
chr19 51693268 51693291 hsa-miR-125a-5p
chr19 20399320 20399342 hsa-miR-1270
chr19 13874910 13874932 hsa-miR-181d-5p
chr19 10817469 10817491 hsa-miR-199a-5p
chr19 28798188 28798210 hsa-miR-3134
chr19 813590 813612 hsa-miR-3187-5p
chr19 18282129 18282151 hsa-miR-3188
chr19 18386570 18386594 hsa-miR-3189-5p
chr19 47226988 47227010 hsa-miR-3190-3p
chr19 47226952 47226974 hsa-miR-3191-3p
chr19 45639009 45639031 hsa-miR-330-3p
chr19 4770700 4770723 hsa-miR-3529-3p
chr19 53787716 53787738 hsa-miR-371a-3p
chr19 53787678 53787700 hsa-miR-371b-3p
chr19 53787931 53787953 hsa-miR-372-3p
chr19 53787895 53787917 hsa-miR-372-5p
chr19 53788748 53788770 hsa-miR-373-3p
chr19 20027075 20027100 hsa-miR-3916
When I used multicov from bedtools
bedtools multicov \
-bams SRR1054203.segemehl_chr19.sam.bam.sorted.bam \
SRR1054204.segemehl_chr19.sam.bam.sorted.bam \
SRR1054205.segemehl_chr19.sam.bam.sorted.bam \
SRR1054206.segemehl_chr19.sam.bam.sorted.bam \
SRR1054207.segemehl_chr19.sam.bam.sorted.bam \
SRR1054208.segemehl_chr19.sam.bam.sorted.bam \
-bed ../genome/chromosome.19_hsa_mature.fasta.bed.out > conteo_mature_hsa_microRNAs
chr19 10552122 10552144 hsa-miR-1238-5p 0 0 0 0 0 0
chr19 51693268 51693291 hsa-miR-125a-5p 0 0 0 0 0 0
chr19 20399320 20399342 hsa-miR-1270 0 0 0 0 0 0
chr19 13874910 13874932 hsa-miR-181d-5p 0 0 0 0 0 0
chr19 10817469 10817491 hsa-miR-199a-5p 0 0 0 0 0 0
chr19 28798188 28798210 hsa-miR-3134 0 0 0 0 0 0
chr19 813590 813612 hsa-miR-3187-5p 0 0 0 0 0 0
chr19 18282129 18282151 hsa-miR-3188 0 0 0 0 0 0
chr19 18386570 18386594 hsa-miR-3189-5p 0 0 0 0 0 0
chr19 47226988 47227010 hsa-miR-3190-3p 0 0 0 0 0 0
chr19 47226952 47226974 hsa-miR-3191-3p 0 0 0 0 0 0
chr19 45639009 45639031 hsa-miR-330-3p 0 0 0 0 0 0
chr19 4770700 4770723 hsa-miR-3529-3p 0 0 0 0 0 0
chr19 53787716 53787738 hsa-miR-371a-3p 0 0 0 0 0 0
chr19 53787678 53787700 hsa-miR-371b-3p 0 0 0 0 0 0
chr19 53787931 53787953 hsa-miR-372-3p 0 0 0 0 0 0
chr19 53787895 53787917 hsa-miR-372-5p 0 0 0 0 0 0
chr19 53788748 53788770 hsa-miR-373-3p 0 0 0 0 0 0
chr19 20027075 20027100 hsa-miR-3916 0 0 0 0 0 0
chr19 804977 804999 hsa-miR-4745-3p 0 0 0 0 0 0
chr19 804941 804963 hsa-miR-4745-5p 0 0 0 0 0 0
chr19 4445987 4446009 hsa-miR-4746-5p 0 0 0 0 0 0
chr19 49933073 49933096 hsa-miR-4751 0 0 0 0 0 0
chr19 58386827 58386849 hsa-miR-4754 0 0 0 0 0 0
What could be the problem? Thank you for your time and consideration
Cordially,
Adriana
Do the BAM files use the same chromosome names (i.e., chr19 rather than 19)? That's a common cause of things like this.
Thanks very much!! it works
Kind regards,
Adriana