Analysis of single end 10x genomics data

Question

[luckysardar171]

Hello I am trying to reanalyze the 98 bp 10x genomics ChromiumTM Single Cell 3’ Reagent Kits v1 data from the SRX3363790 problem is there is no paired end reads are available. 10x genomic tutorial its always mentioned paired end and read1 will have cell and umi info and read2 transcript info please give me some suggestions how can I proceed or i have to contact respective paper authors to get more information about the data

Answer 1

[GenoMax]

If you look under the Data Access tab for the record that you linked above you will find the original BAM file that submitters included. You should be able to convert that using bamtofastq utility (LINK) from 10x to get the proper set of reads. This data is from cellranger v.1.x so you will need to run with following options (replace N with number of threads you want to use).

bamtofastq --nthreads=N --cr11  iPSCs_serum.bam.1 dir_name_you_want