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KChen-lab / Monopogen

SNV calling from single cell sequencing
GNU General Public License v3.0
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Whether SmartSeq data can be used with the Somatic function？ #33

Closed zuoyichen closed 6 months ago

zuoyichen commented 6 months ago

Whether SmartSeq data can be used with the software.SmartSeq sequencing is a single cell, does not provide barcode.csv. Somatic function available?

jinzhuangdou commented 6 months ago

Unfortunately, current monopogen version does not support Smartseq. We are working on monopogen v2.0 to include the long-read module.

zuoyichen commented 6 months ago

Thank you for your reply and look forward to monopogen v2. In the github introduction section, it is mentioned that Smartseq data can be used. In other aspects, the authors feel that it is feasible to use Samtools to manually add barcode to the bam data format of Smartseq, imitates the use of somatic in 10X.

jinzhuangdou commented 6 months ago

Sorry for the confusion. We have removed the smart-seq part in the introduction. It indeed requires new implementation to handle such long read data since they can provide more information. Thanks