Tophat Does not Work with SOLiD Reads

[Fernas]

I have been trying for several weeks to run Tophat on SOLiD reads but I got the same error message every time. While I searched a lot of forums and related questions but could not find a solution.

a sample of my data is:
=====
@SRR179591.60.1 mendel_20110320_FRAG_BC_Ryan_RNA_Seq_2_70_490_F3 length=50
T02213232.20202212300333
+SRR179591.60.1 mendel_20110320_FRAG_BC_Ryan_RNA_Seq_2_70_490_F3 length=50
!<=B?@=7B!8>;@BB<:@-<259
=====

I use Tophat v2.0.13 and the error message that I got is:
=====
[2015-01-22 11:01:43] Beginning TopHat run (v2.0.13)
-----------------------------------------------
[2015-01-22 11:01:43] Checking for Bowtie
Bowtie version: 1.1.1.0
[2015-01-22 11:01:43] Checking for Bowtie index files (genome)..
[2015-01-22 11:01:43] Checking for reference FASTA file
[2015-01-22 11:01:43] Generating SAM header for HumanGenome/Ensemble78/HumanIndexedGenome/Bowtie1ColorSpace//Human
Warning: found a read < 20bp in SRR179592_Trimmed.fastq
[2015-01-22 11:02:06] Reading known junctions from GTF file
[2015-01-22 11:02:55] Preparing reads
left reads: min. length=19, max. length=50, 20533939 kept reads (147 discarded)
Warning: short reads (<20bp) will make TopHat quite slow and take large amount of memory because they are likely to be mapped in too many places
[2015-01-22 11:08:48] Building transcriptome data files TophatAlignment/tmp/Homo_sapiens.GRCh38.78
[2015-01-22 11:10:07] Building Bowtie index from Homo_sapiens.GRCh38.78.fa
[2015-01-22 11:44:10] Mapping left_kept_reads to transcriptome Homo_sapiens.GRCh38.78 with Bowtie
[FAILED]
Error running bowtie:
Too few quality values for read: 1T0B
are you sure this is a FASTQ-int file?
terminate called after throwing an instance of 'int'
========

The command that I used to run Tophat is:
=====
tophat --color --bowtie1 -o out -r 500 --mate-std-dev 500 --no-mixed -p 16 -G Homo_sapiens.GRCh38.78.gtf Bowtie1ColorSpace/Human Reads_Trimmed.fastq
=====

[jcjeong]

Re: Tophat Does not Work with SOLiD Reads

I have same problem.
I added following option as shown in Tophat manual (http://ccb.jhu.edu/software/tophat/manual.shtml)
--library-type secondstrand

This option doesn't work as well.

[intregen]

I have the same problem. Were you ever able to find a solution?

[Michael.Ante]

AFAIK, only Tophat version 1 is capable of aligning colorspace reads.
You need to download and run a much older version than (v2.0.13) from http://ccb.jhu.edu/software/tophat/downloads/

[bardriel]

AFAIK, only Tophat version 1 is capable of aligning colorspace reads.
You need to download and run a much older version than (v2.0.13) from http://ccb.jhu.edu/software/tophat/downloads/

I know this is an old post but in case anyone need it I will post.
You can use TopHat2 but with --bowtie1 parameter. This will use bowtie1 to map the color reads (bowtie2 is not able to do it), so there is no need to download an old TopHat version.