merging PE reads in Single cell transcriptome

Question

[kanwarjag]

I am studying RNA-seq in limited number of cells and have used PE (75bp) to sequence mRNA. Since the data ultimately we get will be very limited. I was wondering will it be useful if I merge both PE reads and use it for further analysis and may improve mapping. I read several tools like BB merge can be used. The aim is to identify signature genes associated with disease based on DE. Any input will be great. Thanks

Answer 1

[mbk0asis]

I don't think merging PE reads and treating as SE reads is not a big concern. You can simply use a command called 'cat' to merge into a single file. I think the mapping efficiency will be improved if the current data contain a lot of unpaired reads, otherwise it won't. You should decide which one to use after mapping the original and merged data.

[kanwarjag]

Thanks. 'Cat' is good to join multiple Fastq. However I am trying to get information from limited amount of single cell data which will be specific and can improve the alignments.

Answer 2

[chen]

If most templates' length are less than 2 * 75, then merging them based on overlap analysis will help.