Announcement

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

  • rwarren
    replied
    you have to specify the hla reference sequence file (-h) at a minimum..

    -h hla fasta file............................<HLA_ABC_CDS.fasta>

    Leave a comment:


  • obricard
    started a topic HLA identification

    HLA identification

    Hello,

    I would like to identify the HLA alleles of some samples sequenced with Solid (50bp single end). My first idea was to extract a sam file containing the reads mapped in HLA locus (using samtools) then convert it in fastq (using picard) and finally use seq2HLA. The problem is that seq2HLA need paired end read. I saw that HLAminer could also do the job. The problem is that I can manage to type a correct command line : I tried : perl HLAminer.pl -a myfile.sam ; but it get this :
    Usage: HLAminer.pl [v1.0.5]
    Derivation of HLA class I and II predictions from Shotgun sequence datasets
    --------------------------------------------------------------------
    HPTASR (HLA Predictions by Targeted Assembly of Shotgun Reads):
    -b blastn alignments.........................<tig_vs_hla-ncbi.coord>
    -r reciprocal blastn.........................<hla_vs_tig-ncbi.coord>
    -c contig fasta file.........................<TASRhla200.contigs>
    -z minimum contig size.......................<200>
    ------------------------------- OR ---------------------------------
    HPRA (HLA Predictions by Read Alignment):
    -a sam alignments............................<ngs_vs_hla.sam>
    --------------------------------------------------------------------
    -h hla fasta file............................<HLA_ABC_CDS.fasta>
    -p P-designation file........................<hla_nom_p.txt>
    -i minimum % sequence identity...............<99>
    -q minimum log10 (phred-like) expect value...<30>
    -s minimum score.............................<1000>
    -n consider null alleles (1=yes/0=no)........<0>
    -l label (run name) -optional-

    Could you help me ?

    Thanks in advance

Latest Articles

Collapse

  • seqadmin
    Multiomics Techniques Advancing Disease Research
    by seqadmin


    New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

    A major leap in the field has
    ...
    02-08-2024, 06:33 AM
  • seqadmin
    The 3D Genome: New Technologies and Emerging Insights
    by seqadmin


    The study of three-dimensional (3D) genomics explores the spatial structure of genomes and their role in processes like gene expression and DNA replication. By employing innovative technologies, researchers can study these arrangements to discover their role in various biological processes. Scientists continue to find new ways in which the organization of DNA is involved in processes like development1 and disease2.

    Basic Organization and Structure
    Understanding...
    01-22-2024, 03:25 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 08:57 AM
0 responses
12 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-14-2024, 09:19 AM
0 responses
43 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-12-2024, 03:37 PM
0 responses
410 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-09-2024, 03:36 PM
0 responses
649 views
0 likes
Last Post seqadmin  
Working...
X