Rna-seq analysis using FASTA file

Question

[Meghna]

I am trying to convert FASTA sequences for SARS CoV-2 from GISAID into read counts matrix for RNA-seq analysis. I tried doing the same on galaxy after assigning dummy scores to my fasta file to convert it to fastqc format and then aligning my reads with hisat 2 to the SARS cov-2 Wuhan genome but when I finally try to find the counts with FeatureCounts and put the Annotation file for SaRS Cov 2 from GENCODE I am not getting any mapped reads. All my reads are showing unmapped. I am really clueless on how to do it.Will be really grateful if someone can help me out

[Ram]

to convert FASTA sequences for SARS CoV-2 from GISAID into read counts matrix

after assigning dummy scores to my fasta file to convert it to fastqc format

Sometimes I feel like the word "convert" needs to be banned on the forum. Can you convert a carrot into a salad? Or a piece of paper into an education? In the same way, you cannot convert a "fasta" into anything. Please use the right words. And when you go on a quest to understand the word you need to describe the process, answers will become clear to you without you having to ask anyone.

[Kevin Blighe]

You mean RNA seq?

[Meghna]

Yes I wanted to do RNA seq analysis with data from GISAID but thats a DNA data so it won't be possible

Answer 1

[GenoMax]

convert FASTA sequences for SARS CoV-2 from GISAID into read counts matrix for Rna seq analysis

What does this mean? You can't use DNAseq data and "convert" it to counts. featureCounts requires gene models to do its counting after alignment of the data. DNAseq data is not going to have expressed parts of the genome.

[Meghna]

Got it.Thanks a ton for the help.