Header Leaderboard Ad

Collapse

MapSplice2 does not recognize my Bowtie indexes

Collapse

Announcement

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

  • MapSplice2 does not recognize my Bowtie indexes

    Hi everybody,

    I wannted to start working with MapSplice2, however, I run into the problem that it does not recognize my Bowtie1 indexes (build using v1.1.1).

    I am using this command:
    python ${PROGRAMDIR}MapSplice-v2.2.1/mapsplice.py -c ${GENOMEDIR}MapSplice -x ${GENOMEDIR}MapSplice/bt1_GRCh38_apr2019 -1 ${READ1}${SUFFIX2} -2 ${READ2}${SUFFIX2} --threads 6 --output ${align_DIR_MapSplice}${READ1:${#SOURCEDIR}:-${#SUFFIX1}-${#PAIR1}}MapSplice.sam

    This code makes mapsplice2 run:
    [Thu Jul 4 06:32:24 2019] Beginning Mapsplice run (MapSplice v2.2.1)
    [Thu Jul 4 06:32:24 2019] Bin directory: /share/tools/MapSplice-v2.2.1/bin/
    [Thu Jul 4 06:32:24 2019] Preparing output location /share/analysis/CEFIC/CEFIC_testdata/HeCaToS_APA/Trimmed_reads_trimmomatic/MapSplice2/APA_MapSplice.sam/
    [Thu Jul 4 06:32:24 2019] Checking files or directory: /share/analysis/CEFIC/CEFIC_testdata/HeCaToS_APA/Trimmed_reads_trimmomatic/APA_The_000_2_R1.fastq
    [Thu Jul 4 06:32:24 2019] Checking files or directory: /share/analysis/CEFIC/CEFIC_testdata/HeCaToS_APA/Trimmed_reads_trimmomatic/APA_The_000_2_R2.fastq
    [Thu Jul 4 06:32:24 2019] Checking files or directory: /share/tools/data/genomes/GRCh38_r96_april2019/MapSplice/
    [Thu Jul 4 06:32:24 2019] Checking Bowtie index files
    [Thu Jul 4 06:32:24 2019] Building Bowtie index for reference sequence


    But it can not find my bowtie1 indexes and tries to build them. Strangely, it actually starts overwriting the indexes I have already created. After about 6 hours, building the indexes fails, returning this error:
    Error: Building Bowtie index files failed /share/tools/data/genomes/GRCh38_r96_april2019//MapSplice/bt1_GRCh38_apr2019.*

    What is wrong with my code?
    How do I get MapSplice to recognize the indezes I build myself?

    Thank you already,
    Marcha

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

ad_right_rmr

Collapse
Working...
X