Header Leaderboard Ad

Collapse

Reference file in MapDamge2

Collapse

Announcement

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

  • Reference file in MapDamge2

    I am new to bioinformatics, so please forgive me for this simple question!
    I am trying to use MapDamage2, and am not sure how to format the reference file. It is currently in .fasta, and was ok the bowtie/samtools pipeline I used, but I don't know how to change it so it works with MapDamage.... any suggestions would be much appreciated.

    $ mapDamage -i /Users/name/IonXpress_..._55.sff.raw.bam -r ref.fasta
    Error: 'ref.fasta' is not a valid file
    Option parsing failed, terminating the program

  • #2
    Originally posted by Cat_J View Post
    I am new to bioinformatics, so please forgive me for this simple question!
    I am trying to use MapDamage2, and am not sure how to format the reference file. It is currently in .fasta, and was ok the bowtie/samtools pipeline I used, but I don't know how to change it so it works with MapDamage.... any suggestions would be much appreciated.

    $ mapDamage -i /Users/name/IonXpress_..._55.sff.raw.bam -r ref.fasta
    Error: 'ref.fasta' is not a valid file
    Option parsing failed, terminating the program
    Maybe try the full path of the file (like what you did for the input file).

    Comment

    Latest Articles

    Collapse

    • 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
    • seqadmin
      AVITI from Element Biosciences: Latest Sequencing Technologies—Part 6
      by seqadmin
      Element Biosciences made its sequencing market debut this year when it released AVITI, its first sequencer. The AVITI System uses avidity sequencing, a novel sequencing chemistry that delivers higher quality data, decreases cycle times, and requires lower reagent concentrations. This new instrument reportedly features lower operating and start-up costs while maintaining quality sequencing.

      Read type and length
      AVITI is a short-read benchtop sequencer that also offers an innovative...
      12-29-2022, 10:44 AM

    ad_right_rmr

    Collapse
    Working...
    X