problem with bedtools

Question

[mra8187]

Dear all i am trying to use bedtools to snp filtering by get the error . what's wrong ?

my script is :

cat '/media/mra/4A3B44B64CA65A93/SNP/DATA/drone-larvae/SRR1571716/Trimmomatic/tophat_out/junctions.bed' \
    | bed_to_juncs | flankBed -g '/home/mra/Downloads/genome_size.txt' -b 1 \
    | slopBed -g '/home/mra/Downloads/genome_size.txt' -b 5 \
    > '/media/mra/4A3B44B64CA65A93/SNP/DATA/drone-larvae/SRR1571716/Trimmomatic/tophat_out/window.bed'

error is :

Warning: malformed line 1, missing columns
     track name=junctions description="TopHat junctions"
ERROR: chrom "1" not found in genome file. Exiting.
Traceback (most recent call last):
  File "/home/mra/miniconda3/bin/bed_to_juncs", line 69, in <module>
    sys.exit(main())
  File "/home/mra/miniconda3/bin/bed_to_juncs", line 59, in main
    print("%s\t%d\t%d\t%s\t%s" % (chromosome, left_pos, right_pos, orientation, counts))
BrokenPipeError: [Errno 32] Broken pipe

Answer 1

[Ram]

Are you sure your input files are built for the same reference genome? This looks like it could be a case of GRCh37 naming vs ucsc hg19 naming conventions (>1,>2,>3,... vs >chr1, >chr2,>chr3,...)

[mra8187]

thanks for your help .... very thanks ..........