Marjan Hosseini issues

Results 4 issues of


                                            Marjan Hosseini

single_to_multi_fast5 do not collect all the single files if the input folder contains mixed types of fast5 files.

I have a dataset that contains thousands of mixed multiple and single fast5 files in a non-homogenous folder structure. I want to convert all the fast5 files to multi fast5...

The results are mapped to an opposite strand than their alignment, does the argument --referenceWindow remains the same for both strands?

The result of ipdSummary of reads that are mapped to a positive strand are shown to be in the reverse strand and vice versa: My reference is mapped to the...

How critical is the "Non-unique read group integer IDs found" warning in running ipdSummary?

I am trying to get the ipdRatio and modified bases information from a PacBio bam file which is sorted and indexed. The command I'm running is: ``` ipdSummary sorted_chr21_0_100000.bam --reference...

ipdSummary command stops working if --identify m5C_TET is included in command, and does not give any m5C info either

I have installed the latest SMRT Tools (ipdSummary version 3.0). My goal is to extract ipdRatio and modified bases. In the ipdSummary --help command I see this instruction: ``` --identify...