Mapsplice commands for fusion gene and which file used ?

Question

[amitunited0532]

I have confused Which file used as reference genome (.fasta, fa, gtf, etc.) Please tell me about exact command with example, if possible.

Answer 1

[archana.bioinfo87]

Hi, For mapsplice you can run this command

python mapsplice.py -p 16 --gene-gtf your_gtf_file.gtf -o Output_directory_name --fusion --min-fusion-distance 200 -c /Dir_of_chromosome/ -x /bowtie_index/ -1 test1_1.fastq -2 test1_2.fastq

It will give you the result. You can also optimize the parameter according to your need.

Hoping it will help you.

[amitunited0532]

Output of mapsplice.

[Sat Aug 4 12:29:43 2018] Beginning Mapsplice run (MapSplice v2.2.0) [Sat Aug 4 12:29:43 2018] Bin directory: /home/prashant/anaconda2/bin/ [Sat Aug 4 12:29:43 2018] Preparing output location outputfusegene/ [Sat Aug 4 12:29:43 2018] Checking files or directory: SRR085725.fastq_filtered [Sat Aug 4 12:29:43 2018] Checking files or directory: genome_index.fa/ Error: Could not find files or directory genome_index.fa/

I am confused which chromosome file used ? (-c /Dir_of_chromosome/) ?

[archana.bioinfo87]

Ok. In this error you had not mentioned your bowtie index file properly. For example I have a test1 sample files

Sample files=test1_1.fastq and test1_2.fastq Dir_of_chromosome= path/where your all chromosome file present/ bowtie index= path/where bowtie index files/prefixname of bowtie index

Suppose I created a bowtie index for hg19 (bowtie-build hg19.fa hg19). I made a folder name like bowtie_hg19. Also, I kept all chromosomes (chr1, chr2, chr3.....etc) file in in a folder name chr_all within a bowtie_hg19 folder.

So, to run mapsplice I will write the command like this

python mapsplice.py -p 16 --gene-gtf your_gtf_file.gtf -o Output_directory_name --fusion --min-fusion-distance 200 -c bowtie_hg19/chr_all -x bowtie_hg19/hg19 -1 test1_1.fastq -2 test1_2.fastq

I think it will help you.