How process non-10X RNA-seq library

[yuanlizhanshi]

I have a batch of self-constructed test data, where UMI and barcode information is located at fixed positions in R1, and R2 contains the sequencing data. I need to append the barcode and UMI information to R2, but in some cases, the library is quite short, and R2 can sequence through into R1. I need to trim the polyA tail in R2 before alignment. Would this type of sequencing data be compatible with preCellar?
The custom library is below.

[yuanlizhanshi]

I should ask in seqspec

[kaizhang]

This can be handled by precellar. But more detailed information about the library is needed, such as the "(9) Final library structure" in this example: https://teichlab.github.io/scg_lib_structs/methods_html/SMART-seq_family.html.

[yuanlizhanshi]

This can be handled by precellar. But more detailed information about the library is needed, such as the "(9) Final library structure" in this example: https://teichlab.github.io/scg_lib_structs/methods_html/SMART-seq_family.html.

I encountered an issue while using the seqspec tool. When attempting to read the local spec.yaml file, an error occurred, preventing the file from being properly accessed. Here are the steps I followed to generate the file:

First, I initialized the sequence specification file with the following command:
seqspec init -o spec_test.yaml -n myassay -m rna -r "rna,R1.fastq.gz,r1_primer,25,pos:rna,R2.fastq.gz,r2_primer,0,neg" "((r1_primer:25,barcode:10,umi:10,cdna:150,r2_primer:0)rna)"
seqspec format spec_test.yaml > spec.yaml

[kaizhang]

I suggest you use the seqspec templates here to start with: https://github.com/regulatory-genomics/precellar/tree/main/seqspec_templates.

Many current seqspec you can find do not conform the seqspec specification/schema: https://github.com/pachterlab/seqspec/blob/main/seqspec/schema/seqspec.schema.json