Question: Picard EstimateLibraryComplexity output file empty
0
gravatar for eggrandio
9 months ago by
eggrandio10
eggrandio10 wrote:

Hi,

I am trying to use the Picard tool "EstimateLibraryComplexity" but, after obtaining my output file, I cannot find any data.

I only get the input conditions I selected, but no output. I am attaching an example:

> ## htsjdk.samtools.metrics.StringHeader
> # picard.sam.markduplicates.EstimateLibraryComplexity INPUT=[PQEG1_wt_D_BAM]
> OUTPUT=/galaxy-repl/main/files/022/016/dataset_22016696.dat
> MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20
> MAX_GROUP_RATIO=500 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0
> ## htsjdk.samtools.metrics.StringHeader
> # Started on: Fri Nov 03 18:30:56 CDT 2017

I have tried different BAM files with the same result. I assume that the results are in file "dataset_22016696.dat", but I do not know how to access it. Am I doing something wrong?

Thanks!

chip-seq • 283 views
ADD COMMENTlink modified 9 months ago by Jennifer Hillman Jackson25k • written 9 months ago by eggrandio10
0
gravatar for Jennifer Hillman Jackson
9 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

This tool required pair-end mapped BAM input for the calculations. Your inputs were single-end.

Hope that helps! Jen, Galaxy team

ADD COMMENTlink written 9 months ago by Jennifer Hillman Jackson25k
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