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chaolinzhanglab / czplib

Chaolin Zhang lab perl library
GNU General Public License v3.0
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some questions about CIMS.pl #3

Closed kir1to455 closed 3 years ago

kir1to455 commented 3 years ago

Hello,when I use CIMS.pl to get the sites, it will have some following problems. 'Inconsistency detected between the tag file and the mutation file. Make sure the NAME column of the two files use the same IDs' I don't know how to solve it, can you give me some advice? Here is my command: perl CIMS.pl -v -n 5 -p -c ./cache_del --keep-cache Mettle3.WT.total.tag.uniq.bed Mettle3.WT.total.tag.uniq.del.bed Mettle3.WT.total.tag.uniq.del.CIMS.txt Mettle3.WT.total.tag.uniq.bed comes from "cat Mettle3.WT.rep1.tag.uniq.bed Mettle3.WT.rep2.tag.uniq.bed > Mettle3.WT.total.tag.uniq.bed"

zhangchaolin commented 3 years ago

One common problem that causes this issue is that the tag IDs in the tag bed file is not unique.

kir1to455 commented 3 years ago

Thanks for your help, the above problems have been successfully solved. However, there are new problems with the cims.pl runtime. ↓ "perl /ctk-1.1.4/simulateCIMS.pl -n 545573 -w 1 -p ./cache_C2T/mutation.pos.txt -srand 1.17082803610629 Mettle3.WT.total.tag.uniq.bed ./cache_C2T/mutation.random.0.bed position < 0? at /ctk-1.1.4/simulateCIMS.pl line 66, <$fin> line 265774. CMD=perl /ctk-1.1.4/simulateCIMS.pl -n 545573 -w 1 -p ./cache_C2T/mutation.pos.txt -srand 1.17082803610629 Mettle3.WT.total.tag.uniq.bed ./cache_C2T/mutation.random.0.bed failed: 6400" Could you give me some advice and suggestions?