Runnig tuxedo with SOLID data (color_space_index)

Question

[Veli Kaan Aydin]

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.

[Devon Ryan]

Did you download the index or did you make it yourself? If you've done neither, then you need to use bowtie-build.

[Veli Kaan Aydin]

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

[Devon Ryan]

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.

[Veli Kaan Aydin]

I understand you thank you for help :)

[Veli Kaan Aydin]

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

[Devon Ryan]

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).

[Veli Kaan Aydin]

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

[Devon Ryan]

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.

[Veli Kaan Aydin]

Hello Devon I need to ask another question to you ;

Let me write log and command 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]
Error running 'prep_reads'
terminate called after throwing an instance of 'int'

This is my fastq file;

@SRR121577.1 head0094_20091130_2_CD8_M14_15_427_13_15_F3 length=35
ATTANAAANNNNNNTNTGCCNNNNNNNGANNNNGG
+
A<%%!!<>!%3*+*!!!().!'6%+02!+!+25!/
@SRR121577.2 head0094_20091130_2_CD8_M14_15_427_13_159_F3 length=35
TATANTACNNNNNNGNTAGTNNNNNNNGCNNNNTA
+
2<%B!!B-!61:(1!!!%%+!2-.&&8!6!(1%!0
@SRR121577.3 head0094_20091130_2_CD8_M14_15_427_13_303_F3 length=35
TACTNAGTNNNNNNGNTTTGNNNNNNNGANNNNCA
+
>B10!!)A!79B>%!!!9'4!@7/63%!%!)</!%
@SRR121577.4 head0094_20091130_2_CD8_M14_15_427_14_630_F3 length=35
ATGCANNNCGCGCGNNTACGCGAGTGTAGATATNN
+
(%'&&!)(!(')%%!%!%%%%'&%%&'%%%%%%!%
@SRR121577.5 head0094_20091130_2_CD8_M14_15_427_15_5_F3 length=35
TATCGNNNCGACTCNNNNNNNNNNNNNNNNNNNTC
+
%8*&4!/1!<2<)%!@;003,+,,-''6*1/%7!)
@SRR121577.6 head0094_20091130_2_CD8_M14_15_427_15_14_F3 length=35
ATAACNNNTTAAAGNNAATGGCGTATAGGTTAANN
+
4=*%;!*6!1&&/)!(!%2',(%(*%+(3'%%)!'
@SRR121577.7 head0094_20091130_2_CD8_M14_15_427_15_160_F3 length=35
TAATANNNGTATTANNGCGTCGGCGATATGTAGNN
+
.B*A6!A)!07>.1!%!4+%&6%%)*2%(%%(%!,
@SRR121577.8 head0094_20091130_2_CD8_M14_15_427_15_301_F3 length=35
TACACNNNCGCGAANNGGTGTAATGTAACGTAANN
+
0B5%;!0=!&%A/%!,!0%%&<3%%%&3%(&&%!(
@SRR121577.9 head0094_20091130_2_CD8_M14_15_427_17_7_F3 length=35
TATCGCGAATCAATNNNNNNNNNNNNNNNNNNNGC
+
%?010?)*'=%2*%!?8'(.(&)*%'%''1(2/!-
@SRR121577.10 head0094_20091130_2_CD8_M14_15_427_17_1697_F3 length=35
ATATGNNNNNNNNNTATAAGTGTTGTGTCATGTNN
+
(%%+)!.%%)')+*!%''%%%&%%5%'%&(%(%!%
@SRR121577.11 head0094_20091130_2_CD8_M14_15_427_20_19_F3 length=35
TATGTTATACTAACTGTGTGAACCGACATGGCTNN
+
'<2>1.65A269<4*1050'4/%9(4:(63;,%!0
@SRR121577.12 head0094_20091130_2_CD8_M14_15_427_20_35_F3 length=35
ATCTGCGGCATTCANNNNNNNNNNNNNNNNNNNGA
+
'?%%'&6%%%&8%%!&'%%%%<%%%%&%'%%%%!%
@SRR121577.13 head0094_20091130_2_CD8_M14_15_427_20_37_F3 length=35
TAGACGCTCCTTATCGCAGACGAGGTTGTCACTNN
+
3A'*)(2%%(%;(&,''-+%%=&%%(*%%%*%'!,
@SRR121577.14 head0094_20091130_2_CD8_M14_15_427_21_3_F3 length=35
ATGCATACGCGGGCCGTAGTCGGTACTCCTCACTC
+
%6'')3*(%.(%&*%+%%%%%%%%'%%(('%%%%&
@SRR121577.15 head0094_20091130_2_CD8_M14_15_427_23_19_F3 length=35
TATGTTATATATTGATGTCAGCGCGCTGCGGCTAT
+
,@4&.1>%?&&?/*(*+(%(%%&%&*%%-'1%+%%
@SRR121577.16 head0094_20091130_2_CD8_M14_15_427_23_82_F3 length=35
TCTGTATTATGGACTACGTGCTATAGCACCACTCG
+
,%'*.()%%%('%%'('%%&(%%%&%%%%%(%)%&
@SRR121577.17 head0094_20091130_2_CD8_M14_15_427_23_1713_F3 length=35
ATGCATACGCATATGTGTAGCGACTCGCAGTGATC
+
%%'&()))*(%)%&%%)&)%%'%%%%(&%%%%%&%
@SRR121577.18 head0094_20091130_2_CD8_M14_15_427_24_17_F3 length=35
TAGTGGCGCGCGGCTACTGTTACAAAAGCATCTAG
+
:<((6,?(=*'>(%%+.%%%%&'%%%(%%(%*/&&
@SRR121577.19 head0094_20091130_2_CD8_M14_15_427_24_1420_F3 length=35
ATGACGCATATAGACGTGAGCGTGCTTACATAGAC
+
'%(%%()()'))%+%)%%%%&%'%%%+&%%%%%%(
@SRR121577.20 head0094_20091130_2_CD8_M14_15_427_25_354_F3 length=35
CTGCTTTGTTTACCTGAGCAAGAAGTTTACCGTGA
+
BBABBBBB=BBBB<BA>@>?@B%1A>?)<?=@>)<
@SRR121577.21 head0094_20091130_2_CD8_M14_15_427_25_1696_F3 length=35
ATGTGCGTATATCGTAGTAGATAGCGTGAGACCGA
+
%9%(&%&'-&()%%%&%%%%%'*%%%%%%%%%*%%
@SRR121577.22 head0094_20091130_2_CD8_M14_15_427_27_116_F3 length=35
TCACATACGCCGGATATCTCGGGTGTTCTGTGATC
+
-8+',&.)((&(,&%)*%%%%%,%(&(&*%**,%,
@SRR121577.23 head0094_20091130_2_CD8_M14_15_427_27_269_F3 length=35
TCATGCGTCGGCCGATTCTTATCGTGACGTCTAGT
+
-,%%)'()%'%'%%%(&%%%%%%%%,%%%%.+%%%
@SRR121577.24 head0094_20091130_2_CD8_M14_15_427_28_43_F3 length=35
AGCATATCTCGTCCAGACTCATAAACCTCATGAGT
+
%>22'7>++%7A;*-<*;9.)/1,(-<&0%();%1
@SRR121577.25 head0094_20091130_2_CD8_M14_15_427_28_58_F3 length=35
TGCAAATGGCTTGGTACCCAACTCTTTCCGGTCTT
+
@-549=0*-B*)2%:)9:6-748<3)&1(9/('03
@SRR121577.26 head0094_20091130_2_CD8_M14_15_427_28_119_F3 length=35
TTCTGCTGCGTAAACGTTCGTGCATTCCCAATCCT
+
>=3)&*%'*%(&*%%,1'&%*)&%).%*%'*%+%)
@SRR121577.27 head0094_20091130_2_CD8_M14_15_427_28_154_F3 length=35
TCTCATAGGCATTCGCTAGATACTGTAAGCAAGAC

Do you see any problem?

[Devon Ryan]

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

[Veli Kaan Aydin]

Ok I understand that, thank you :)