ensemble illumina tissues aligned rnaSeq

Question

[fk566938]

Hello, I found bam files of the 16 tissue set RNA-seq data illumina put out on the european nucleotide archive here at this website called "ensembl" --> ftp://ftp.ensembl.org/pub/release-78...ens/genebuild/ . I was wondering if anyone knew if these bam files are already sorted. Somebody is helping me on monday plot some coordinates of an isoform of a gene my PI is working on and I think these bam files are supposed be .bam.bam files when they are sorted? I am not sure what .bai files are either. Is there an easier way to find tissue expression or specificity of a gene isoform that is not widely regarded in the databases? My PI wants this data asap.

Answer 1

[mkulecka]

https://www.ebi.ac.uk/gxa/experiments/E-MTAB-513 - here you can find processed data from experiment you mentioned.

If you have samtools installed, you can easily check if bam files are sorted:

samtools view -H you_bam_file.bam  | grep SO

For instance, if you get SO:coordinate as result, it means files are sorted by coordinates.

Bai files are bams' index files.