Header Leaderboard Ad


Solid-color space indexing for human fasta file



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

  • Chipper
    Try with a longer index, I think the recommended were between 12-14 long? 5 bases with no open positions does not make much sense for human. Masking strategies are described in the publications/documentations.

    Leave a comment:

  • Solid-color space indexing for human fasta file

    I am using BFAST for indexing color space data using the command:

    bfast index -f folder/human_bfast.fa -m '11111' -w 5 -A 1 -n 8

    If I try to index the fasta file with a few chromosomes, say till 17, the tool successfully creates .bif file. But if I use a bigger fasta file (ie. from chr 1 till 22) for indexing then the tool throws error:

    Currently on [contig,pos]:
    Sorting by thread...
    100.000 percent complete************************************************************
    In function "RGIndexMergeHelperFromDiskContig_8": Fatal Error[ReadFileError]. Message: Could not read in tmp lower.
    The file stream error was:: Bad file descriptor
    ***** Exiting due to errors *****
    I want to create solid color space index for human fasta for all chromosomes from 1 through 22, X,Y

    Please note that the step just prior to indexing (ie. creating reference in color space using the same fasta) was always successful. It creates .fa.cs.brg file successfully.
    Can anybody please help me with the problem ?

    Thanks in advance,

Latest Articles


  • seqadmin
    A Brief Overview and Common Challenges in Single-cell Sequencing Analysis
    by seqadmin

    ​​​​​​The introduction of single-cell sequencing has advanced the ability to study cell-to-cell heterogeneity. Its use has improved our understanding of somatic mutations1, cell lineages2, cellular diversity and regulation3, and development in multicellular organisms4. Single-cell sequencing encompasses hundreds of techniques with different approaches to studying the genomes, transcriptomes, epigenomes, and other omics of individual cells. The analysis of single-cell sequencing data i...

    01-24-2023, 01:19 PM
  • seqadmin
    Introduction to Single-Cell Sequencing
    by seqadmin
    Single-cell sequencing is a technique used to investigate the genome, transcriptome, epigenome, and other omics of individual cells using high-throughput sequencing. This technology has provided many scientific breakthroughs and continues to be applied across many fields, including microbiology, oncology, immunology, neurobiology, precision medicine, and stem cell research.

    The advancement of single-cell sequencing began in 2009 when Tang et al. investigated the single-cell transcriptomes
    01-09-2023, 03:10 PM