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MGI-tech-bioinformatics / DNBelab_C_Series_HT_scRNA-analysis-software

An open source and flexible pipeline to analysis high-throughput DNBelab C Series single-cell RNA datasets
MIT License
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final.bam convert to fastq file #46

Closed Gordonlu66 closed 5 months ago

Gordonlu66 commented 9 months ago

Hello, I have a final.bam file, and i want to convert bam file back to the paired raw fastq file. So that i can re map agin. I try to use samtools fastq, but it can not output paired fq file correctly. Further, i tried software bamtofastq, and it is useful to convert bam to fastq file in 10X scRNA-seq data. but it is fail to convert bam file generated by DNBelab_C platform. how can i do that in DNBelab_C platform. looking forward to your reply. thank you!

lishuangshuang0616 commented 9 months ago

Sorry, we don't have that feature yet. We discard reads that do not align and their quality scores when generating the BAM file. Fully restoring the raw reads is currently not feasible. @Gordonlu66

lishuangshuang0616 commented 9 months ago

https://github.com/shiquan/PISA Use the PISA command PISA bam2fq to convert to single-ended @Gordonlu66 image