Question: Unable to convert single cell RNA Seq bam to fastq using cellranger's bamtofastq
gravatar for Researcher
11 weeks ago by
Researcher50 wrote:

Hi i have a quick question, i have few aligned bam files from single cell RNA Seq data. I want to regenerate fastqs from them. In order to do so i am using cellranger's bamtofastq and I am also getting fastq files but in the specified path within a folder named “MissingLibrary_1_flowcellName”. I am not sure what does this mean? Why the generated folder is named as missing library. Does anybody have any idea about this?

The command I used is:

cellranger bamtofastq possorted_genome_bam.bam ./sample

Any help will be highly appreciated.


ADD COMMENTlink modified 11 weeks ago • written 11 weeks ago by Researcher50
gravatar for genomax
11 weeks ago by
United States
genomax84k wrote:

I don't think this is correct. There is no option available in cellranger to conver BAM files to fastq.

You should just run bamtofastq utility that 10x provides to do this on its own. See more info here. If you are using this utility and test data that they provide then it does indeed make data folders with names such as indepth_C05_MissingLibrary_1_HL5G3BBXX. Not sure why that is so but the data works without any problems.

ADD COMMENTlink modified 11 weeks ago • written 11 weeks ago by genomax84k

Thanks @genomax for your response. Yes I am using the same bamtofastq utility. Earlier with some previous set of data and the same command I was able to generate fatsq files in folders named with their unique ID but this time the same command has generated with “MissingLibrary” named folder.

That’s why I am more concerned and still looking for an explanation.

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by Researcher50

My hunch is this may have something to do with the way cellranger was originally run. If a SampleName was not provided during the run it may generate this type of names when BAM files are reconverted. You may want to send a ticket in to 10x support to see what their response is and then post it here.

ADD REPLYlink written 11 weeks ago by genomax84k
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