Developing Oyster Male Gonad Gene Expression Tracks¶

Attempting to develop IGV genome browser tracks from Zhang et al data.

Overview

1. Track based on transcript specific expression¶

Table is available in SQLShare https://sqlshare.escience.washington.edu/sqlshare#s=query/sr320%40washington.edu/Mgo_RNAseq_transcript

Description:

Paired end Male Gonad RNA-Seq data from Zhang et al 2012 Exported file from CLCL v6
Data provided at exon level
Derived using Dataset:
Zhang, G; Fang, X; Guo, X; Li, L; Luo, R; Xu, F; Yang, P; Zhang, L; Wang, X; Qi, H; Zhu, Y; Yang, L; Huang, Z (2012): Genomic data from the Pacific oyster (Crassostrea gigas). GigaScience. http://dx.doi.org/10.5524/100030          
          Maximum paired distance = 250
          Unspecific match limit = 10
          Minimum exon coverage fraction = 0.2
          Count paired reads as two = No
          Additional downstream bases = 0
          Minimum paired distance = 180
          Minimum similarity fraction = 0.8
          Additional upstream bases = 0
          Strand = Forward
          Use annotations for gene and transcript identification = Yes
          Organism type = EUKARYOTE
          Minimum length fraction (long reads) = 0.9
          Minimum read count fusion gene table = 5
          Exon discovery = Yes
          Expression level = Transcripts
          Create report = Yes
          Use colorspace encoding = No
          Expression value = RPKM
          Create list of unmapped reads = No
          Create fusion gene table = No
          Minimum number of reads = 10
          Maximum number of mismatches allowed (applies to short reads) = 2
          References = oyster.v9_90-7
          Use strand specific assembly = No
          Minimum length of putative exons = 25
          Expression value = Read Per Kilobase of exon Model value
Found: 25123 genes.
Total number of reads : 54739722 ( single reads: 0, paired reads: 54739722 )
Total number of mapped reads : 25685813 ( single reads: 0, paired reads: 25685813 )
Total number of unmapped reads : 29053909 ( single reads: 0, paired reads: 29053909 )
    ```

_Screenshot_

<img src="https://www.evernote.com/shard/s10/sh/7cf328c4-581f-4038-bd35-f0d62ccc81b4/a0bd8da1cd6c088cc2f5a6d751a111f7/deep/0/Screenshot%205/29/13%202:28%20PM.jpg" alt="Screenshot%205/29/13%202:28%20PM" Width = 50% />

Query

Screenshot

Downloading via python client

python fetchdata.py -d "[sr320@washington.edu].[Mgo_RNAseq_transcript_IGV]" -f tsv -o /Volumes/web/cnidarian/Mgo_RNAseq_transcript.igv

http://eagle.fish.washington.edu/cnidarian/Mgo_RNAseq_transcript.igv

Sorted within IGV

This creates a new file http://eagle.fish.washington.edu/cnidarian/Mgo_RNAseq_transcript.sorted.igv

Seems to have worked but not certain on coordinates...