Sicer outputting No such File, warning and Directory
Hi I have been using sicer to see if I can get a better peak call on the H3k27me3. I converted my BAM files, which have already been aligned via BWA to bed file.
I used the line of code below the example given:
Example: /SICER-rb.sh ["InputDir"] ["bed file"] ["OutputDir"] ["species"] ["redundancy threshold"] ["window size (bp)"] ["fragment size"] ["effective genome fraction"] ["gap size (bp)"] ["E-value"]
My code (editted the file names to fit):
SICER-rb.sh MP2_input.bed MP2_H3K27me3.bed folder_1 hg19 1 200 150 .8 600 100
The code seems to run fine but it keeps outputting an error indicating that chromosomes can't be read. I keep getting lines that look like the ones below:
warning: chrY reads do not exist in MP2_input.bed/MP2_H3K27me3.bed
Warning: chr1 reads do not exist in /gpfs/gsfs4/users/bimas_ltg/Histone_ChIPseq_2016/scriptsMEM.cmd/MACS/SCICER/scicer_files/MP2_Merge_H3K27me3-1-removed.bed
Thank you for your help !
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Do you get anything when you do
grep chrY MP2_input.bed/MP2_H3K27me3.bed?if I do grep MP2_input.bed or grep MP2_H3k27me3 it works; however, the error also says that their is not such file for grep chrY MP2_input.bed/MP2_H3K27me3.bed
Since those two are
warning'sit may be fine to proceed. You don't have data for those two chromosomes in those two files.I would proceed but the files outputted are mostly blank.