I have a set of metatranscriptomics sequence samples. Let's say the following sample fastq file is what I have. I would like to map these reads to a bacterial genome assembly identified by the link, https://www.ebi.ac.uk/ena/browser/view/GCA_009849585.1
My objective is to get a count profile of genes/functions mapping to the above genome. I am grateful to you if you can show me the right direction to accomplish this task.
My idea is to use bowtie2 to map any reads to the reference genome and get a bam file. And, then to use featurecounts to get an abundance profile. Am I on correct path or am I missing something?
@K00348:93:HKCH2BBXX:5:1101:26362:1701 1:N:0:NTGAAA GAAATACGATTGATATGTATTTTCATAACAAAGTATTCTAATGCAATTGTCCTTTTTAATATCATTAAAAAA + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @K00348:93:HKCH2BBXX:5:1101:26362:1701 2:N:0:NTGAAA TTTTTTAATGATATTAAAAAGGACAATTGCATTAGAATACTTTGTTATGAAAATACATATCAATCGTATTTC + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @K00348:93:HKCH2BBXX:5:1101:4422:1842 1:N:0:NTGAAA CAAGAGTGACGGCAGAGAAATGCCGGACCCGGCCACCCAGCGACACTGGGCAACCCATTCAGGGTTTTGATGGCCAAACTATCCGCCAGC + JJJJJJJJFJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJFJJJFJ<JJJ7JJJJJJJFJJJFJJJJJJ @K00348:93:HKCH2BBXX:5:1101:4422:1842 2:N:0:NTGAAA ATCGGTCGTCAAGCGACCCAGGGACCCCGGCGTGGCGCGAACAAGCTGGCGTGATCGTTTGGTATGCAGAGCTGGCGGATAGTTTGGCCA + JJJJJJJJFJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJJ7FJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ