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Error Running 'prep_reads' Top Hat

Has anyone coded a fix for this? Trinity command for paired sequences (Illumina) Dear all, I ran Trinity to create a de novo alignment of two paired files an... I am using MAC OSX10.11.4. The awk command solution that you used assumes that a fastq record is distributed over four lines. navigate here

Tophat-Fusion Error 'Long_Spanning_Reads' I have run Tophat fusion with paired-end RNA-Seq data, but my run was unsuccessful. I followed the awk command from here to extract all reads of length 75: Filtering Fastq Sequences Based On Lengths I also did the tophat on the original fastq file (before The error is not very helpful for me to know what... tophat -o t...

if possible help me. The first line contains the header, second lines contains the sequence, third line is usually the + sign, and the fourth line contains quality sequence. Tophat2 Reporting output tracks failed I am working on analysing some RNA sequence data using tophat2. Tophat Error : Couldn't build bowtie index with err = 1 I used the following command to run tophat  tophat -G $RPATH/ED.gtf -o $RPATH/tophat/E1 ...

Although I'm very inexperienced with bioinformatics, what I"m trying to do is very straightforwar... Thanks Zohra Saci alignment bowtie samtools bam • 1000 views ADD COMMENT • link • Not following Follow via messages Follow via email Do not follow modified 5.1 years ago by Tophat qual length error. The fact that TopHat is choosing a seed length of 101bp tells me something's up with that file.

Hi all,  I ran tophat on my fastq file and I got the following error: [2015-09-02 11:23:58] Beg... The Illumina sequence file uses '.' for undetermined bases and prep_reads filters this out when reading the sequence. 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. Error running 'prep_reads' on TopHat (v2.0.9) Hello everyone, Using "tophat -p 8 -G genes.gtf -o c1_R1_thout genome SRR121576.fq SRR121577.fq"...

I used default parame... 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 Often this means a Phred score is out of range.

Tophat Question: No Accepted_Hits.Bam Generated I am using tophat to map the SOLiD single-end 50mer reads to S.cerevisae genome. Thanks Clariet Quote: Originally Posted by Cole Trapnell Thanks for the heads up. Hi! but encountered some errors.

ERROR on tophat: Mapping left_kept_reads to genome Athaliana with Bowtie2 I kept get this error when running tophat. http://qtechnology.net/error-running/error-running-env-gem-path-global.html ERROR on tophat: Mapping left_kept_reads to genome Athaliana with Bowtie2 I kept get this error when running tophat. Tophat Slow : Searching For Junctions Via Segment Mapping Hi, Is it normal that my tophat jobs are running the step "Searching for junctions via segment m... Tophat Hi, I am running galaxy locally and when I perform alignments with TopHat I get the following ...

Error running bowtie: .. (When I use tophat2) Hi I was install bowtie2(apt-get install bowtie, bowtie2, samtools) and version is /usr/bin/b... One last thing though: I do see an extra newline at the end of the sample you posted, so I would double check your input file once to make sure that testset_0_F5.qual >1_104_494_F5 7 6 12 12 17 13 4 5 5 13 7 10 5 7 12 9 5 4 4 5 4 4 -1 7 6 4 4 -1 -1 http://qtechnology.net/error-running/error-running-javac-exe.html TopHat's FASTQ parser occasionally screws up when FASTQ records are incorrectly formatted or when the read and/or quality sequences span more than one line in the file.

Hi All, I was mapping paired end fastq files by tophat2 on 10 threads, it got stucked during Sea... but encountered some errors. Tophat error!

ADD REPLY • link modified 2.3 years ago • written 2.3 years ago by Devon Ryan ♦ 58k When I tried that command it just gave me TopHat index.

hi friends, i was running the tophat2 but i got error...do you know the reason please? [[email protected].. 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... Error while running Tophat 2.0.11 Hi everyone, I have a problem in running tophat 2.0.11 with a 50 bp paired end illumina RNA read... 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 ...

TopHat Fata Error: Fusion search fails with Bowtie2, how to try Bowtie1 option? I... I downloa... http://qtechnology.net/error-running/error-running-compiler.html This may be what is upsetting tophat.

I tried but it did not work. this is my entire command: tophat -o /storage/gwajnberg/outputtopha... The seed length ought to be 25 for 50bp reads or longer. ADD REPLY • link modified 14 months ago • written 14 months ago by Ashutosh Pandey ♦ 10k 0 14 months ago by Ashutosh Pandey ♦ 10k Philadelphia Ashutosh Pandey ♦

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. TopHat: Error: Couldn't build bowtie index with err = 1 Hi I'm trying to run TopHat on a Cloudman Galaxy instance and I keep getting the below error. what is the mean of 'Error running 'prep_reads' ??? Could anybody help?