[DZhang]

Hi Michael.James.Clark,

Thank you for the clarfication. I did not know actually the difference was clearly documented. I learn a few new things in this field every day!

This may be suited for a new thread but what's your view on duplicate removal for single-end reads?

Regards,
Douglas

https://www.contigexpress.com

[shruti]

Hi Michael,
Thanks for the info. I was not aware of this limitation of rmdup.
Will try Picard and see. (and next time I would be cautious of the filenames I write)

Hi Dzhang,
Thanks for the info on your pipeline.

[Glouglou14]

Hi,

I'm also facing the same problem here is case in question. The read names are same.

HWI-ST220_63:6:2108:11340:115090 177 chr1 14480159 37 50M chr5 84273185 0 GCTACCACTCAGAAACTTGGAGAAATCACAGAGAGCCATGGACTTTATTT JIIHGIGJIJJIJHGIHGGJJJJJJJJIJJJIJJJIJGHHHHFFFFFCCC XT:A:U NM:i:0 SM:i:37 AM:i:3X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:50
HWI-ST220_63:6:2108:11340:115090 113 chr5 84273185 37 50M chr1 14480159 0 AACAGAATTCCAGTGAGATACCTTCTTCCTTCTCAGGATTTTACATGTTA HHJIJJIIIJJJJJJJJIHDJJJIJIJJJJJIIJJJJHHHHHDFFFFCCC XT:A:U NM:i:0 SM:i:3AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:50
HWI-ST220_63:6:1108:12937:121403 177 chr1 14480159 37 50M chr5 84273185 0 GCTACCACTCAGAAACTTGGAGAAATCACAGAGAGCCATGGACTTTATTT JIIGJIHGJJJJIHGJJJIJJJJJJIJHJIJIJJJIJHHHFHFFFFFCCC XT:A:U NM:i:0 SM:i:37 AM:i:3X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:50
HWI-ST220_63:6:1108:12937:121403 113 chr5 84273185 37 50M chr1 14480159 0 AACAGAATTCCAGTGAGATACCTTCTTCCTTCTCAGGATTTTACATGTTA JJIIJIJIGJJGIIJJIGE;JJJJIIJJJJIIIJJJJHFHHHFFFFFCCC XT:A:U NM:i:0 SM:i:3AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:50

Any pointers would be most appreciated.

I had the same issue than shruti. Here is how i fixed it (in case is usefull for someone else...).
Samtools rmdup was having trouble with "supplementary alignment". I removed them (samtools view -b -F 0x0800 foo.bam > foo.noSupAln.bam) and everything went fine.

[Momina]

hi
from which file we have to remove duplicates either from file.bam or file.sorted.bam?

[dpryan]

It's simplest to remove duplicates from a sorted BAM file (in fact, most tools require that the input is sorted).