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Error Running 'prep_reads' Top Hat

I'm new to scripting,... Tophat Question: No Accepted_Hits.Bam Generated I am using tophat to map the SOLiD single-end 50mer reads to S.cerevisae genome. Content Search Users Tags Badges Help About FAQ Access RSS Stats API Use of this site constitutes acceptance of our User Agreement and Privacy Policy. There happens to be a '@' in the quality scores after 90 and prep_reads treats it as the start of a new record, and this messes up the next record and http://venamail.com/error-running/error-running-discovery-citrix.html

Any thoughts? Tophat Error: Segment-Based Junction Search Failed With Err Hello, I have run several analysis with Tophat 2 on my local instance of galaxy and I get this er... Hello everyone;   I'm trying to rna-seq analysis for Illumina Genome Analyzer (Homo sapiens) an... Error: Could not find Bowtie 2 index files (p.*.bt2) Hi, I am repeating alignments using TopHat, I am using the same Bowtie index as I used previousl...

Hi! Tophat Fails At Mapping Right_Kept_Reads To Genome With Bowtie I already used Tophat some times, but now I changed my script so it could handle xsq format. I am surprised that I am the first one to encounter this problem. I am also getting seed lengths = read_length (54, 76bp).

Hi All, I was mapping paired end fastq files by tophat2 on 10 threads, it got stucked during Sea... Low final mapping rate by TopHat in spite of high initial Bowtie mapping Hi,  I am running TopHat2/2.0.14 using this code: tophat \ --transcriptome-index "${tra... Input FASTQ files were filtered using R ShortRead package. I ran into a common bug on Chrome, where users downloading large files will often have incomplete files.

Checked with the lab corrected these (20, 20), but still got no splices. about • faq • rss Community Log In Sign Up Add New Post Question: Error running 'prep_reads' on TopHat (v2.0.9) 0 2.3 years ago by Veli Kaan Aydin • 20 Turkey Do I still need to use --solexa-quals? Tophat-Fusion Error 'Long_Spanning_Reads' I have run Tophat fusion with paired-end RNA-Seq data, but my run was unsuccessful.

running tophat+cufflinks but result in 0 FPKMs Hi: I am running tophat+cufflinks to analyze a RNA-seq dataset downloaded from GEO[1] below is ... The error say... Hi all,  I ran tophat on my fastq file and I got the following error: [2015-09-02 11:23:58] Beg... Hi All, I was mapping paired end fastq files by tophat2 on 10 threads, it got stucked during Sea...

Issue with alignement using Tophat2/Bowtie2 on MiRNA deep sequencing HI I am trying to use Tophat2/Bowtie2 to align MiRNA from NGS to whole mouse genome. I am assuming it worked for you. bzhang View Public Profile Send a private message to bzhang Find More Posts by bzhang 05-06-2010, 06:30 AM #19 maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Can anyone comment on if this is a safe workaround?

TopHat error during aligning reads I use tophat to analyze RNA-seq DATA on my Macbook Pro(RAM, 8GB) ,but there is an error: 201... http://venamail.com/error-running/error-running-env-ldflags-l-opt-sm-pkg-active-lib.html tophat error help I was running tophat using galaxy in amazon cloud and I git this error, someone can help me to fi... ERROR on tophat: Mapping left_kept_reads to genome Athaliana with Bowtie2 I kept get this error when running tophat. Error In Tophat This is the error I am getting while running Tophat.

tophat Preparing reads [FAILED] Why is tophat giving this error message? Thank you.   error rna-seq tophat • 1.6k views ADD COMMENT • link • Not following Follow via messages Follow via email Do not follow modified 2.3 years ago by Devon Can someone help? get redirected here Segment-based junction search error keeps coming up.

ADD REPLY • link modified 4.4 years ago • written 4.4 years ago by samsara • 460 thanks i already installed zlib. Thanks in advance!   rna-seq tophat illumina • 475 views ADD COMMENT • link • Not following Follow via messages Follow via email Do not follow modified 11 months ago • How To Run Phrap With Quality Score Input I tried the following command: ./phrap/phrap.manyreads Sample.fasta Sample.qual -ace But it ...

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Segment-based junction search error keeps coming up. Tophat 2 alignment error Hello everyone, I am trying to aligned a paired end sequences using tophat2. I am having a trouble with... Write Failure In Tophat 1.3.1 X86_64 using tophat 1.3.1 x86_64...

The fact that TopHat is choosing a seed length of 101bp tells me something's up with that file. Tophat qual length error. m... useful reference First of all, ...

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