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bcgsc / rnabloom2_manuscript

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rnabloom benchmarking analysis #1

Open dvirdi01 opened 1 year ago

dvirdi01 commented 1 year ago

I assembled my long-read transcriptome files through rna bloom. I was wondering what the best way to analyze it is? I want to retrieve information like reads per gene, see how it matches with my reference genome etc.... I saw that the bloom transcripts.fa file needs to be aligned with minimap2 as such:

Align read to RNA-Bloom2 assembly (minimap2 2.24-r1122): minimap2 -t 16 -a -x map-ont rnabloom.transcripts.fa READS.fastq | \ samtools sort -T ./tmp -O bam -o aln.bam samtools index aln.bam samtools flagstat aln.bam > aln.bam.flagstat

but I was confused on what exactly the READS.fastq file is? Are those the sample long-read fastq files or the reference genome file?

kmnip commented 1 year ago

I was confused on what exactly the READS.fastq file is? Are those the sample long-read fastq files or the reference genome file?

Those commands were used to align the reads to the assembly to determine the percentage reads aligned to the assembly. READS.fastq is the same file containing the input reads that was used for the assembly.