Cel-seq requires custom processing as it has barcodes to identify cells, so just aligning the whole file and counting over genes is not enough. Are you aware? Use something like Alevin https://salmon.readthedocs.io/en/latest/alevin.html
Is Cel-seq & Cel-seq2 protocols are with Strand specific library .If so should i use Stranded 'yes' option in HT-Seq-Count
From the cel-seq paper it is mentioned >97% are from one strand reads.Still i have a confusion about the strandedness of the library
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Parichitran •
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I myself found the answer. Yes cel-seqs are strand specific.Since Htseq-count default already is for strand option=yes.So I can run with or without mentioning the strand parameter.
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Parichitran •
yeah ATpoint,Even my data has umi barcodes too .Currently I am using zUMIs for processing my data which handled it all.But I got a doubt regarding Stranded option in that pipeline.Since Celseq protocol group's inhouse pipeline used HT-Seq-Count.So asked the above question with HT-Seq-Count,Just to understand it clearly. Thanks a lot for your concern :)
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