Error with dba.count function code
1
0
Entering edit mode
VCLRAC001 • 0
@vclrac001-14183
Last seen 3.9 years ago

Hi

I am analyzing ATAC-seq data for several embryonic replicates. An extract of my sample sheet looks as follows:

Sample ID    Tissue    Replicate    BamReads    Peaks    PeakCaller
Sample1    FL    1.1    /home/stark/Documents/Rachelle/sample1_trimmed_rmdup_bowtie2_mapped.bam    /home/stark/Documents/Rachelle/sample1_trimmed_rmdup_bowtie2_mapped_macs2_peaks.bed    bed

I made a Correlation Heatmap without any problem, but when trying to do a read count with dba.count it keeps giving me the following error:
Error in pv.counts(DBA, peaks = peaks, minOverlap = minOverlap, defaultScore = score,  :
  Can't count: some peaksets are not associated with a .bam file.

I tried a truncated version of my sample sheet, different file paths, and different bam and bed files in various combinations. Every time I get stuck at the same step. Is there anything else I could try?

Thanks for any advice in advance
- L

diffbind dba.count atac-seq • 473 views
ADD COMMENT
0
Entering edit mode
Gord Brown ▴ 640
@gord-brown-5664
Last seen 8 months ago
United Kingdom

Hi

Try changing the column name from "BamReads" to "bamReads".  It's case sensitive, and yes, it's inconsistent with the other column names...

Cheers,

 - Gord

ADD COMMENT

Login before adding your answer.

Traffic: 443 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6