MyronBest
commented
2 years ago Dear Emberwhirl, thank you for reaching out. We employed Samtools v1.115. As far as I am aware we never had this issues ourselves. Perhaps run the script line by line, esp. regaring the samtools steps, and see what is the problem here. Perhaps Ed in cc, you have additional suggestions?
The thromboSeq pipeline can also be applied to paired-end RNA-seq data. For this some manual adjustments have to be made to the pipeline, e.g. the paired-end function of trimmomatic, supplying two input files to STAR, etc. If you need help for that, let us know.
Best wishes, Myron
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Op 29 okt. 2021, om 17:56 heeft Emberwhirl @.**@.>> het volgende geschreven:
Hello. I am currently following your Nature Protocols paper to analyze RNAseq data for platelets. I would like to know if you have any suggestions on applying your pipeline to paired-end RNAseq data.
Also, what is the version of Samtools used in this pipeline? When I run this pipeline, it would mostly stop at the Samtool step right after the completion of the Picard-tool step and throw out a manual page of Samtool sort function. No error message is shown.
Thank you very much.
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Hello. I am currently following your Nature Protocols paper to analyze RNAseq data for platelets. I would like to know if you have any suggestions on applying your pipeline to paired-end RNAseq data.
Also, what is the version of Samtools used in this pipeline? When I run this pipeline, it would mostly stop at the Samtool step right after the completion of the Picard-tool step and throw out a manual page of Samtool sort function. No error message is shown.
Thank you very much.