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.
Thanks
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.
My hunch is this may have something to do with the way
cellranger
was originally run. If aSampleName
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.