Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • how to use galaxy tool interval_maf_to_merged_fasta.py

    I want to use the stitcher to extract a given region from MAF files, stitch
    it together and convert it to FASTA.

    I downloaded and installed Galaxy according to the instructions from


    I believe the actual stitcher is "interval_maf_to_merged_fasta.py" in the
    /tools/maf directory (not clear from the paper or docs but I belive this is
    the tool that implements this functionality).

    How can I actually extract, stitch, convert with
    interval_maf_to_merged_fasta.py?

    I have difficulties figuring all necessary command line parameters out by
    reading the source code.

    F.e. here I tried to get the stiched FASTA conversion for a region defined
    in "foo.bed" out of "chr1.maf":
    python /pub1/lvyl2012/software/lyl/galaxy/tools/maf/interval_maf_to_merged_fasta.py /pub1/lvyl2012/ExtractMultipleAlignment/mulAlign/chr1.maf -d hg17 -t cached -c 1 -s 2 -e 3 -S 6 -p hg17 -m /pub1/lvyl2012/ExtractMultipleAlignment/mulAlign/ -z /pub1/lvyl2012/software/lyl/galaxy/tool-data/ -i /pub1/lvyl2012/ExtractMultipleAlignment/aa.bed -o /pub1/lvyl2012/ExtractMultipleAlignment/results.fa

    It gives the error mssage:

    The MAF source specified (/pub1/lvyl2012/ExtractMultipleAlignment/mulAlign/) appears to be invalid



    Is it necessary to index the MAF files first somehow? Do I have to set the
    type of MAF file, and to what?

    Would be great if someone could give a short overview how to stitch MAF
    files command-line based.

Latest Articles

Collapse

  • seqadmin
    Exploring the Dynamics of the Tumor Microenvironment
    by seqadmin




    The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
    07-08-2024, 03:19 PM
  • seqadmin
    Exploring Human Diversity Through Large-Scale Omics
    by seqadmin


    In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
    06-25-2024, 06:43 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 07-10-2024, 07:30 AM
0 responses
23 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-03-2024, 09:45 AM
0 responses
200 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-03-2024, 08:54 AM
0 responses
209 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-02-2024, 03:00 PM
0 responses
192 views
0 likes
Last Post seqadmin  
Working...
X