DeepTools Error: Be sure that the bam files you are using is indexed.
1
0
Entering edit mode
8.6 years ago
dally ▴ 210

I am attempting to use the bamCorrelate function of deeptools to find the reproducibility between two chip seq replicates.

I have used samtools index BAMFILE to index my files, but I am still running into this error so I must not be doing this correctly.

Here is the command I used for deeptools

bamCorrelate bins \
  --bamfiles /Volumes/mydata/2015108/IDRM/2015_10_21_0/analysis_results/Sample_Pol_II_9_29/Alignments/Pol_II_9_29.mapped.rgid.sorted.filtered.dups_remove.bam.bai \
  /Users/jonathanreeder/carlos-projects/Dropbox/ChIP-Seq/hg19/old_data/Sample_Pol-II-Chip-N20/Alignments/Pol-II-Chip.mapped.rgid.sorted.filtered.dups_remove.bam.bai \
  -out pol-correlation

Here's the error:

Be sure that the bam file you areusing is indexed.
deeptools • 3.2k views
ADD COMMENT
3
Entering edit mode
8.6 years ago
matted 7.8k

You are giving it the index files (*.bam.bai), when you should probably be giving it the bam files (*.bam).

ADD COMMENT
0
Entering edit mode

Ahh I see. I fixed that and was able to run the command line just fine. However, I can't seem to get it to work when running the --corMethod pearson parameters. It keeps telling me that it is an unrecognized argument. But everything on the github has the parameters written exactly like this. Any ideas?

The --plotFile command appears to be unrecognized as well.

ADD REPLY
0
Entering edit mode

I'm not sure. Maybe you have an old version installed?

ADD REPLY

Login before adding your answer.

Traffic: 2516 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