SNP Discovery error

Question

[a.hasankhani74]

hi I want to create a bed file from bowtie-inspect summary and the TopHat output file with the bed extension, so a new bed-format file is generated that defines a 5-base-pair window around each junction of the slots(In the SNP discovery workflow): (this command)

cat Analysis/tophat/junctions.bed | Analysis/RNA-seq/bed_to_juncs | flankBed -g genome_size.txt -b 1 | slopBed -g geenome_size.txt -b 5 > window.bed

but I got this error:

ERROR: chrom "1" not found in genome file. Exiting.
Traceback (most recent call last):
  File "Analysis/RNA-seq/bed_to_juncs", line 69, in <module>
    sys.exit(main())
  File "Analysis/RNA-seq/bed_to_juncs", line 59, in main
    print "%s\t%d\t%d\t%s\t%s" % (chromosome, left_pos, right_pos, orientation, counts)
IOError: [Errno 32] Broken pipe

whats the problem?

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

[a.hasankhani74]

This a head of my genome file:

1 dna:chromosome_group chromosome_group:Amel_4.5:1:1:29893408:1 REF 29893408
2 dna:chromosome_group chromosome_group:Amel_4.5:2:1:15549267:1 REF 15549267
3 dna:chromosome_group chromosome_group:Amel_4.5:3:1:13234341:1 REF 13234341
4 dna:chromosome_group chromosome_group:Amel_4.5:4:1:12718334:1 REF 12718334
5 dna:chromosome_group chromosome_group:Amel_4.5:5:1:14363272:1 REF 14363272
6 dna:chromosome_group chromosome_group:Amel_4.5:6:1:18472937:1 REF 18472937
7 dna:chromosome_group chromosome_group:Amel_4.5:7:1:13219345:1 REF 13219345
8 dna:chromosome_group chromosome_group:Amel_4.5:8:1:13546544:1 REF 13546544
9 dna:chromosome_group chromosome_group:Amel_4.5:9:1:11120453:1 REF 11120453
10 dna:chromosome_group chromosome_group:Amel_4.5:10:1:12965953:1 REF   12965953
11 dna:chromosome_group chromosome_group:Amel_4.5:11:1:14726556:1 REF   14726556
12 dna:chromosome_group chromosome_group:Amel_4.5:12:1:11902654:1 REF   11902654
13 dna:chromosome_group chromosome_group:Amel_4.5:13:1:10288499:1 REF   10288499
14 dna:chromosome_group chromosome_group:Amel_4.5:14:1:10253655:1 REF   10253655
15 dna:chromosome_group chromosome_group:Amel_4.5:15:1:10167229:1 REF   10167229
16 dna:chromosome_group chromosome_group:Amel_4.5:16:1:7207165:1 REF    7207165

What should I do now?
please help me.

[Ram]

It's pretty ironic that you replied to my "Please use code formatting" comment with text that is unformatted. Please put in more effort so we don't have to clean up your content while trying to help you.

Answer 1

[ATpoint]

chrom "1" not found in genome file. Exiting. There is no chromosome called 1 in the genome file. Make sure nomenclature is the same, so e.g. chr1 in all relevant files instead of 1.

[a.hasankhani74]

This not work. please more help me

[ATpoint]

Output of head junctions.bed?

[a.hasankhani74]

no.head of bowtie-inspect. the junction.bed is symphonic with cat command. the source of problem is in genome file obtained from bowtie-inspect.but I cant solve it.

[Ram]

ATpoint is asking for the head of junctions.bed. What do you mean by "symphonic"?

[ATpoint]

Type head junctions.bed into your terminal and show the output.

[a.hasankhani74]

here you are:

1       216982  225458  JUNC00000001    3       ?       216982  225458  255,0,0 2       64,71   0,8405
1       216983  225404  JUNC00000002    1       +       216983  225404  255,0,0 2       63,17   0,8404
1       225527  225753  JUNC00000003    7       ?       225527  225753  255,0,0 2       50,68   0,158
1       225529  225717  JUNC00000004    3       +       225529  225717  255,0,0 2       48,32   0,156
1       225723  225913  JUNC00000005    3       +       225723  225913  255,0,0 2       49,56   0,134
1       225727  225913  JUNC00000006    4       ?       225727  225913  255,0,0 2       45,56   0,130
1       225857  226001  JUNC00000007    1       +       225857  226001  255,0,0 2       56,11   0,133
1       225857  226010  JUNC00000008    2       ?       225857  226010  255,0,0 2       56,20   0,133
1       226014  226196  JUNC00000009    2       +       226014  226196  255,0,0 2       46,64   0,118
1       226029  226209  JUNC00000010    3       ?       226029  226209  255,0,0 2       31,77   0,103

[a.hasankhani74]

give your email address or skype ID to me.I want to speak with you for this subject

[Ram]

This is a forum powered by volunteers to help people not just individually but also collectively by addressing problem faced by many people. Spending energy on issues caused by individual circumstances takes away from this community effort.

If you'd like individualized help, please seek out a bioinformatician near you, or see if you can hire/contract one. Soliciting private help from volunteers is unprofessional and rude.

[Kevin Blighe]

We are volunteers here, and you should not expect our time outside of the confines of this website. Please keep the discussion in this thread.