transcript2aminoAcid.md

#Different code for how to run program This is a github created for scripts that can help out in analysing de novo assembled transcriptomes.

For each script or file that is generated please write a nice markdown

https://help.github.com/articles/github-flavored-markdown/

##ORF finder

In:

test.fa (nt)

Out:

test.info (table) test.peptide.fa (aa) test.ORFs.fa (cds) test.523prime.fa (transcript 5 to 3 prime)

Code:

    java -jar /glob/johanr/bin/HTStools.jar -p sequencehandling orfs -i test.fa

##Mapping of reads

in:

reads + reference file

out:

counts per contig per reads file ()

code:

  module load bioinfo-tools
  module load bowtie2/2.2.3
  module load samtools

  bowtie2  --threads 16 -x {REFfile} -1 {ReadsDir}/{sample}_1.fastq -2 {ReadsDir}/{sample}_2.fastq --un-conc {ResultDir}/{sample}.noHit.fastq -S {ResultDir}/{sample}.sam


  samtools view -bSh -o {ResultDir}/{sample}.bam {ResultDir}/{sample}.sam

  samtools sort {ResultDir}/{sample}.bam {ResultDir}/{sample}.sorted 

  samtools index {ResultDir}/{sample}.sorted.bam

  samtools flagstat {ResultDir}/{sample}.sorted.bam > {ResultDir}/{sample}.sorted.flagstat

  samtools idxstats {ResultDir}/{sample}.sorted.bam > {ResultDir}/{sample}.sorted.idxstats

##Rfam using Infernall

Information on how to run the latest version of Infernall is found here.

http://infernal.janelia.org/

Especially the book chapter that goes through every step is found here.

http://selab.janelia.org/publications/Nawrocki13/Nawrocki13-preprint.pdf

##Pfam using HMMer

in:

fastaFile, RFAM_database

out:

fastaFile.PfamAB.hmm.hmmer

module load bioinfo-tools
module load hmmer/3.1b1-gcc

hmmscan --tblout test_0.PfamAB.hmm.hmmer /glob/johanr/references/Pfam/PfamAB.hmm test.fa