Closed weir12 closed 4 years ago
Hi @weir12
no worries, here is a link to download the PTGBase listed genes. It is a shame that the website is down. I may upload the files to the github repo as well:
https://drive.google.com/open?id=1RWhZo8-tTEZ8L4o87X1tW4rGyzMZvvvj
The annotation as downloaded from the Araport website had chromosomes labelled Chr1 Chr2 Chr3... ChrC ChrM whereas the TAIR10 fasta file had chromosome names 1, 2, 3... Mt, Pt. I renamed the contigs in the Araport GTF to match. So it depends where you got your reference sequences from.
thanks a lot !
By the way ,Is the bam file required by thechimera_pipeline
the output of this rule?
https://github.com/bartongroup/Simpson_Barton_Nanopore_1/blob/1b509454a9e25a8c81be5092f8e525ca00e7b5a5/pipeline/nanoPARE_pipeline/Snakefile#L101
no the nanoPARE pipeline is for the analysis of nanoPARE 5' tag data from Schon et al. 2018 which we use to benchmark the adapter filtered full-length reads in figure 5 of the eLife paper. You should not use STAR to map nanopore DRS reads, use minimap2. The rules for this are in the basecalling pipeline.
Hi: Sorry for disturbing you again. I have noticed that A blacklist(contains tandem genes of tair) is required for filtering false positives during chimeric RNA detection in pipeline.
Araport11_GFF3_genes_transposons.201606.no_chr.gtf
mean GTF with the first column(seq_id
) removed ?Thanks again weir