Tophat and colorspace error #Solid #csfasta #length of quality string does not match

[vishalthapar]

Hi All,

A lot of people have asked this but there seems to be no resolution on this so far. I am getting this error and after going through all the posts of CS alignment with tophat, i am still clueless. Any help is appreciated. Thanks in advance. Here is the code and the error:

tophat --quals --color --bowtie1 --output-dir ./output/tophat_align/178-17/ --GTF /data/aryee/pub/genomes/igenomes6_14_13/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf /data/aryee/pub/genomes/igenomes6_14_13/Mus_musculus/Ensembl/NCBIM37/Sequence/BowtieIndex/color_genome /data/aryee/ting/single_cell_rnaseq/mouse_pancreas/input/csfasta/178-17.csfasta /data/aryee/ting/single_cell_rnaseq/mouse_pancreas/input/csfasta/178-17.QV.qual

[2013-08-13 14:34:20] Beginning TopHat run (v2.0.8)
-----------------------------------------------
[2013-08-13 14:34:20] Checking for Bowtie
		  Bowtie version:	 0.12.9.0
[2013-08-13 14:34:20] Checking for Samtools
		Samtools version:	 0.1.18.0
[2013-08-13 14:34:21] Checking for Bowtie index files
[2013-08-13 14:34:22] Checking for reference FASTA file
[2013-08-13 14:34:22] Generating SAM header for /data/aryee/pub/genomes/igenomes6_14_13/Mus_musculus/Ensembl/NCBIM37/Sequence/BowtieIndex/color_genome
	format:		 fasta
[2013-08-13 14:34:54] Reading known junctions from GTF file
[2013-08-13 14:35:05] Preparing reads
	[FAILED]
Error running 'prep_reads'
Error: length of quality string does not match sequence length (0) for color read 1_2_17_F3!

This is my input csfasta:

>1_2_17_F3
T33303212213033320131232210313230100023020222202202
>1_2_282_F3
T03112111021023110221333302301223223033001233322321
>1_2_1483_F3
T01033111001322022312013201121012022111023212200203
>1_2_1488_F3

and this is the QV file:

>1_2_17_F3
31 30 31 17 31 21 31 31 30 31 29 31 31 31 31 31 31 29 31 30 28 31 31 31 31 31 31 31 31 31 31 27 29 31 14 31 31 31 28 31 17 31 31 14 31 14 31 30 17 26 
>1_2_282_F3
28 31 31 31 31 31 31 31 21 31 31 31 31 31 31 31 31 31 31 31 31 31 31 31 31 31 31 26 31 31 31 31 31 31 31 30 14 31 21 31 31 31 31 31 31 29 30 31 28 21 
>1_2_1483_F3
31 31 30 31 31 31 31 31 31 31 31 31 31 31 31 31 27 31 31 31 31 28 31 31 31 31 29 31 31 31 31 31 28 31 31 31 31 31 14 31 31 14 29 31 31 21 17 31 17 31

Thanks again!

-Vishal