Runnig tuxedo with SOLID data (color_space_index)
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7.2 years ago

Hello everyone,

I'm trying to run tuxedo pipeline on ubuntu. But I need to use color command to get the results (  I am not sure if it is correct way to analyze SOLID data). Common usage: tophat --color --quals [other options]* <colorspace_index_base> <reads1_1[,...,readsN_1]> [reads1_2,...readsN_2] <quals1_1[,...,qualsN_1]> [quals1_2,...qualsN_2] I know that but here is my problem; I do not know how to find colorspace_index_base or is there a way for change the solid fastq to illumina fastq.

Thanks.

RNA-Seq tuxedo error solid solid data rna • 1.8k views
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Did you download the index or did you make it yourself? If you've done neither, then you need to use bowtie-build.

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I search and I did not find now I'm doing bowtie-build ( bowtie-build -C SRR121576.fastq SRR121576)

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Ah, you can go ahead and stop that command, it's not what you want. You'll need to either download an index from iGenomes (I assume the files include colorspace indices, but I don't know that for sure), or download the reference genome from UCSC/Ensembl/etc. and use bowtie-build with that.

Since you're very new to this, I'd recommend trying to find someone locally to help you out a bit (that'll get you finished with your analysis a bit more quickly). Alternatively, try to find a course that goes through some of the basics. I know there are some offered in Germany by ecSeq, and I presume there's something similar in Turkey.

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I understand you thank you for help :)

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Devon, Can you write me the reasons of "Error running 'prep_reads' terminate called after throwing an instance of 'int' "  I already download hg 18 colorspace from Bowtie web site and

I fastq-dump some solid SRR (rna-seq) and "tophat -C -o output --bowtie1 colorindex SRR.fastq

And do you see any thing wrong in this code? because it still gives the error

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It's unclear. Perhaps post a couple lines for the SRR.fastq file. Hopefully someone more versed in colorspace will see this, since I pretty much never use colorspace datasets (they're pretty antiquated these days).

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thanks for everything. Is there any pipeline that I can use analyzing SOLID data that you suggest?

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That's unfortunately not something I have enough experience with to offer any advice. Tophat should work, but if it's not then finding out why may not be trivial unless you can code.

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Hello Devon I need to ask another question to you ;

Let me write log and commmand after I'll add my files first lines.;

/rnaseq\$ tophat --bowtie1 --color -p 8 -G genes.gtf -o output_yenisra77 hg18_c yenisra77.fastq

[2014-08-23 22:33:13] Beginning TopHat run (v2.0.12)
-----------------------------------------------
[2014-08-23 22:33:13] Checking for Bowtie
Bowtie version:     1.1.0.0
[2014-08-23 22:33:13] Checking for Samtools
Samtools version:     0.1.19.0
[2014-08-23 22:33:13] Checking for Bowtie index files (genome)..
[2014-08-23 22:33:13] Checking for reference FASTA file
Warning: Could not find FASTA file hg18_c.fa
[2014-08-23 22:33:13] Reconstituting reference FASTA file from Bowtie index
Executing: /home/veli/calisma/bwt1/bowtie-inspect hg18_c > output_yenisra77/tmp/hg18_c.fa
[2014-08-23 22:35:52] Generating SAM header for hg18_c
[2014-08-23 22:36:28] Reading known junctions from GTF file
[2014-08-23 22:36:30] Preparing reads
[FAILED]
terminate called after throwing an instance of 'int'

This is my fastq file;

ATTANAAANNNNNNTNTGCCNNNNNNNGANNNNGG
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A<%%!!<>!%3*+*!!!().!'6%+02!+!+25!/
TATANTACNNNNNNGNTAGTNNNNNNNGCNNNNTA
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2<%B!!B-!61:(1!!!%%+!2-.&&8!6!(1%!0
TACTNAGTNNNNNNGNTTTGNNNNNNNGANNNNCA
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>B10!!)A!79B>%!!!9'4!@7/63%!%!)</!%
ATGCANNNCGCGCGNNTACGCGAGTGTAGATATNN
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(%'&&!)(!(')%%!%!%%%%'&%%&'%%%%%%!%
TATCGNNNCGACTCNNNNNNNNNNNNNNNNNNNTC
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%8*&4!/1!<2<)%!@;003,+,,-''6*1/%7!)
ATAACNNNTTAAAGNNAATGGCGTATAGGTTAANN
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4=*%;!*6!1&&/)!(!%2',(%(*%+(3'%%)!'
TAATANNNGTATTANNGCGTCGGCGATATGTAGNN
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.B*A6!A)!07>.1!%!4+%&6%%)*2%(%%(%!,
TACACNNNCGCGAANNGGTGTAATGTAACGTAANN
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0B5%;!0=!&%A/%!,!0%%&<3%%%&3%(&&%!(
TATCGCGAATCAATNNNNNNNNNNNNNNNNNNNGC
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%?010?)*'=%2*%!?8'(.(&)*%'%''1(2/!-
ATATGNNNNNNNNNTATAAGTGTTGTGTCATGTNN
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(%%+)!.%%)')+*!%''%%%&%%5%'%&(%(%!%
TATGTTATACTAACTGTGTGAACCGACATGGCTNN
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'<2>1.65A269<4*1050'4/%9(4:(63;,%!0
ATCTGCGGCATTCANNNNNNNNNNNNNNNNNNNGA
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'?%%'&6%%%&8%%!&'%%%%<%%%%&%'%%%%!%
TAGACGCTCCTTATCGCAGACGAGGTTGTCACTNN
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3A'*)(2%%(%;(&,''-+%%=&%%(*%%%*%'!,
ATGCATACGCGGGCCGTAGTCGGTACTCCTCACTC
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%6'')3*(%.(%&*%+%%%%%%%%'%%(('%%%%&
TATGTTATATATTGATGTCAGCGCGCTGCGGCTAT
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,@4&.1>%?&&?/*(*+(%(%%&%&*%%-'1%+%%
TCTGTATTATGGACTACGTGCTATAGCACCACTCG
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,%'*.()%%%('%%'('%%&(%%%&%%%%%(%)%&
ATGCATACGCATATGTGTAGCGACTCGCAGTGATC
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%%'&()))*(%)%&%%)&)%%'%%%%(&%%%%%&%
TAGTGGCGCGCGGCTACTGTTACAAAAGCATCTAG
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:<((6,?(=*'>(%%+.%%%%&'%%%(%%(%*/&&
ATGACGCATATAGACGTGAGCGTGCTTACATAGAC
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'%(%%()()'))%+%)%%%%&%'%%%+&%%%%%%(
CTGCTTTGTTTACCTGAGCAAGAAGTTTACCGTGA
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BBABBBBB=BBBB<BA>@>?@B%1A>?)<?=@>)<
ATGTGCGTATATCGTAGTAGATAGCGTGAGACCGA
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%9%(&%&'-&()%%%&%%%%%'*%%%%%%%%%*%%
TCACATACGCCGGATATCTCGGGTGTTCTGTGATC
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-8+',&.)((&(,&%)*%%%%%,%(&(&*%**,%,
TCATGCGTCGGCCGATTCTTATCGTGACGTCTAGT
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-,%%)'()%'%'%%%(&%%%%%%%%,%%%%.+%%%
AGCATATCTCGTCCAGACTCATAAACCTCATGAGT
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%>22'7>++%7A;*-<*;9.)/1,(-<&0%();%1
TGCAAATGGCTTGGTACCCAACTCTTTCCGGTCTT
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@-549=0*-B*)2%:)9:6-748<3)&1(9/('03
TTCTGCTGCGTAAACGTTCGTGCATTCCCAATCCT
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>=3)&*%'*%(&*%%,1'&%*)&%).%*%'*%+%)
TCTCATAGGCATTCGCTAGATACTGTAAGCAAGAC

Do you see any problem ??

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Those aren't colorspace reads, I wonder if they tried converting them to base-space (a bad idea) before uploading.

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Ok I understand that,  thank you :)