Align RNA-seq time series data (Apul)

sr320 commented 1 month ago

Take time series data that is from A pulcra and align to "new" genome using Hisat.

Genome: https://gannet.fish.washington.edu/seashell/bu-github/deep-dive-expression/D-Apul/data/Apulcra-genome.fa https://gannet.fish.washington.edu/seashell/bu-github/deep-dive-expression/D-Apul/data/Apulcra-genome.fa.fai

Gff: https://gannet.fish.washington.edu/seashell/bu-github/deep-dive-expression/D-Apul/data/Apulcra-genome.gff

sr320 commented 1 month ago

note A pulcra is ACR in https://github.com/urol-e5/timeseries_molecular/blob/main/data/rna_metadata.csv (colony ID)

kubu4 commented 1 month ago

Which repo should code go in? deep-dive-expression or timeseries_molecular?

sr320 commented 1 month ago

timeseries_molecular - the repo this issue is in - thanks!

kubu4 commented 1 month ago

Also, is this repo going to be multi-species, like deep-dive? I'm asking so that we can get things organized before we start adding too many files to the existing directory structure.

sr320 commented 1 month ago

yes will be multi species.

On Fri, Oct 4, 2024 at 11:38 AM kubu4 @.***> wrote:

Also, is this repo going to be multi-species, like deep-dive? I'm asking so that we can get things organized before we start adding too many files to the existing directory structure.

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kubu4 commented 1 month ago

Alignments complete.

Full output from alignments (excluding BAMS) is here:

https://github.com/urol-e5/timeseries_molecular/tree/main/D-Apul/output/02.20-D-Apul-RNAseq-alignment-HiSat2

Will be adding/updating README later today.

There's a subdirectory for each sample, containing individual alignments and alignment info, as well as Ballgown-formatted table files.

MultiQC alignment report (GitHub):

https://github.com/urol-e5/timeseries_molecular/blob/main/D-Apul/output/02.20-D-Apul-RNAseq-alignment-HiSat2/multiqc_report.html

DESeq2 count matrices (raw):

StringTie GTF (raw):

Apulchra-genome.stringtie.gtf

Currently rsync-ing repo to have access to BAMS. Will report back when that's complete.