getting coverage by reads metrics

[sumitra20]

Hi @andrewprzh ,

I have an assembled metaT.fasta file and the 32 pairs of raw reads (.fq) that i used for the assembly. I would like to use rnaquast to get the coverage by reads metrics to understand the alignment statistics. How do i go about it? Im pretty confused with the term 'reference genome' as i dont have any? and running the command below only gives me the basic metrics. Did appreciate if you can advice me on the types of useful metrics i can look at using only the assembled file and the raw reads. Also how do i provide more than 1 sequences for the '--left' and '--right' parameter (separating them with ',' gives me error, or shall i create a text file with all the path)?

rnaQUAST.py -c BS_3_trinity_OUT.Trinity.fasta --left_reads R11P4_BS_clean_fwd.fq.gz --right_reads /R11P4_BS_clean_rev.fq.gz --left_reads R13P1_BS_clean_fwd.fq.gz --right_reads R13P1_BS_clean_rev.fq.gz --lower_threshold 50 --upper_threshold 95 --meta --busco bacteria --gene_mark --prokaryote --threads 8

thank you

[andrewprzh]

Hi @sumitra20

rnaQUAST was initially designed as a tool for testing de novo assemblers with the use of reference genome and annotation. So if you don't have them, resulting report might be quite short.

As alternative I can suggest you trying TransRate or DETONATE, which are mostly focused on read-based quality assessment.

Also how do i provide more than 1 sequences for the '--left' and '--right' parameter (separating them with ',' gives me error, or shall i create a text file with all the path)?

I think currently the only way is to concatenate all files together.

Best Andrey