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merging PE reads in Single cell transcriptome

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

rna-seq pe
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updated by chen chen • written by kanwarjag kanwarjag

2 answers

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.

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written by mbk0asis mbk0asis

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.

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written by kanwarjag kanwarjag

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

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written by chen chen

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