Tag Archives: bam

Genes (RNA-Seq) on Oly Genome

We currently have a version (0.0.2) of the Ostrea lurida genome on CoGe. This is 38 scaffolds greater than 80k bp. Below is an effort to map gonad RNA-seq data to said genome.

Two male gonad and two female libraries were mapped to the genome using TopHat in Cyverse Discovery Environment.
cy_1CEA6C82.png

Through the steps…

CoGe__My_Data_1CEA6505.png


CoGe__My_Data_1CEA6557.png

I moved the data in Discovery Environment to coge_data directory.

CoGe__My_Data_1CEA6688.png

Will see what Expression Analysis does…

CoGe__My_Data_1CEA66F8.png

Some output

CoGe__My_Data_1CEA6A27.png

This created two files and corresponding tracks: read depth and BAM alignment

JBrowse_scaffold5824_3156__8360_1CEA6B71.png

Will crank out other three libraries and soon will work on rough annotation.

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Wayback to just-MBD

Prior to bisulfite sequencing we did do a couple of MBD enrichment libraries to describe DNA methylation in oysters. Results even were snuck into this perspective.

mbd

While I am sure there are genome tracks around, I am ending up #doingitagain.

In short I took the raw Solid reads, align to Crassostrea_gigas.GCA_000297895.1.26.dna.genome in CLC, exported bam, converted to bedgraph, converted to tdf.


In long:
The raw files
raw

1) Imported into CLC v8.0.1

          Discard read names = Yes
          Discard quality scores = No
          Original resource = /Users/sr320/data-genomic/tentacle/solid0078_20110412_FRAG_BC_WHITE_WHITE_F3_SB_METH/solid0078_20110412_FRAG_BC_WHITE_WHITE_F3_QV_SB_MOTH.qual
          Original resource = /Users/sr320/data-genomic/tentacle/solid0078_20110412_FRAG_BC_WHITE_WHITE_F3_SB_METH/solid0078_20110412_FRAG_BC_WHITE_WHITE_F3_SB_MOTH.csfasta

(yes the core called them MOTH)

2) Reads were mapped

mapped

3) Exported as BAM.

4) Converted to bedgraph

!/Applications/bioinfo/bedtools2/bin/genomeCoverageBed 
-bg 
-ibam /Users/sr320/data-genomic/tentacle/solid0078_moth.bam 
-g /Volumes/web/halfshell/qdod3/Cg.GCA_000297895.1.25.dna_sm.toplevel.genome 
> /Users/sr320/data-genomic/tentacle/MBD-meth.bedgraph          

5) Converted to toTDF

tdf


Rinse and repeat with unmethylated fraction (UNMOTH) and import tdf into IGV!

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