User: clizama

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clizama0
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Posts by clizama

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Fr-unstranded vs Fr-first strand
... Just curiosity: I know some Library preps kits are Strand specific and others no. In the case of strand specific, for example FR-First strand What happen if I do a analysis using FR-unstraded and FR-first strand for the same data using top-hat. I should have different numbers of count with HT- ...
rna-seq written 8 days ago by clizama0 • updated 7 days ago by Kevin Blighe1.1k
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Comment: C: tophat error help
... Yeah I'm working in try to change the number of threads, my problem is Im runing tophat in galaxy and I couldnt find the option to change the number of threads from 8 to 1. ...
written 18 months ago by clizama0
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Comment: C: RNAseq problems with tophat
... I'm trying to find how to do it. still working on it. ...
written 18 months ago by clizama0
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tophat error help
... I was running tophat using galaxy in amazon cloud and I git this error, someone can help me to fix it. ``` [2016-03-24 07:39:10] Checking for Bowtie Bowtie version: 2.2.3.0 [2016-03-24 07:39:10] Checking for Bowtie index files (genome).. Found both Bowtie1 and Bowtie2 indexes. [2016-03-24 07:39:1 ...
rna-seq written 18 months ago by clizama0 • updated 18 months ago by Ram12k
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Comment: C: RNAseq problems with tophat
... I'm running the tophat from galaxy I'm not sure how to change the number of threads? Can you explain me a little more please Thanks carlos ...
written 18 months ago by clizama0
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Comment: C: RNAseq problems with tophat
... I added the full error ...
written 18 months ago by clizama0
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Comment: C: RNAseq problems with tophat
... 2016-03-24 07:39:10] Checking for Bowtie Bowtie version: 2.2.3.0 [2016-03-24 07:39:10] Checking for Bowtie index files (genome).. Found both Bowtie1 and Bowtie2 indexes. [2016-03-24 07:39:10] Checking for reference FASTA file [2016-03-24 07:39:10] Generating SAM header for /data/refs/mm10/genome.fa ...
written 18 months ago by clizama0
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Answer: A: RNAseq problems with tophat
... [2016-03-24 07:39:10] Beginning TopHat run (v2.0.13) ----------------------------------------------- [2016-03-24 07:39:10] Checking for Bowtie Bowtie version: 2.2.3.0 [2016-03-24 07:39:10] Checking for Bowtie index files (genome).. Found both Bowtie1 and Bowtie2 indexes. [2016-03-24 07:39:10] ...
written 18 months ago by clizama0
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RNAseq problems with tophat
... HI I'm working with a RNAseq pair end dataset. I'm running tophat in galaxy using the amazon cloud. My problem is when I ran tophat I was able to analyze just the half of the data (6 files). For some reason with the other 6 files tophat showed me this msn: error An error occurred with this datase ...
rna-seq written 18 months ago by clizama0 • updated 8 weeks ago by akhilesh0

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