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.
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!
hi friends, i was running the tophat2 but i got error...do you know the reason please? [[email protected]
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?
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