User: GPR

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GPR310
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310
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Mexico
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6 years, 10 months ago
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Posts by GPR

<prev • 106 results • page 1 of 11 • next >
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Can Trinity (de novo) be coupled to Tophat?
... Hello, I understand that Trinity data can be post-processed with Bowtie and later with RSEM. Nature protocols 8.8 (2013): 1494-1512. I would like to know if anybody has processed Trinity assembled fasta file with TopHat or HHSplicer? Thanks, GP ...
assembly alignment written 4.3 years ago by GPR310
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E-Box Promoters In Gene List
... Hello, I have a list of genes up- and downregulated from a couple of mRNA-seq data-sets; and would like to explore if these lists are enriched in E-box containing promoters. Any suggestions on what tool is the most reliable? Thanks, GP. ...
enrichment motif written 5.4 years ago by GPR310 • updated 5.4 years ago by B. Arman Aksoy1.2k
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Answer: A: Vcf File --> Gene/Protein Mutation Information
... A while ago I was recommended the BEDOPs tools, which coupled to a RefFlat-Genes table, will append a gene name per chromosome location. ...
written 5.7 years ago by GPR310
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Cuffmerge Error
... Hello, I have been running Cufflinks/Cuffmerge/Cuffdiff for quite a while, have updated it several times and never had a problem. I typically use the Refseq genes.gtf file for my analysis but recently have started to use a known-Genes-UCSC.gtf file, which I have downloaded from the UCSC tables and ...
written 5.8 years ago by GPR310
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Strand Specific Tophat Output
... Hello, I am having a hard time coming about the possible bad quality of a data-set I just got. The library is paired-end and strand-specific (first strand), and so, I have aligned with TopHat, including the option "--library-type=fr-strand-specific. My problem is that after the Cufflinks/Cuffdiff p ...
written 6.0 years ago by GPR310 • updated 5.6 years ago by Biostar ♦♦ 20
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A-To-G Rna-Editing Vcf File Repository
... Does anybody know where can I get *vcf files from the latest RNA-editing (A-to-G variants) papers? I would like to use one such vcf file in a GATK analysis, similar to how I would use the dbSNP.vcf or the Mills-100G-indels.vcf ones. Thanks, G. ...
vcf written 6.2 years ago by GPR310
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Comment: C: Aligning Paired-End Reads In Single-End Mode
... Comment appreciated, thanks. ...
written 6.2 years ago by GPR310
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Comment: C: Can Tophat Be Used For Mapping Dna-Seq (Whole Genome) Data
... I agree with JC in that TopHat is not a gapped read aligner. In TopHat the computational segmentation of the unaligned reads precedes a second round of alignment guided by known splice junctions. In other words, my understanding is that TopHat aims at aligning reads across gaps created by splicing e ...
written 6.2 years ago by GPR310
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Aligning Paired-End Reads In Single-End Mode
... Hello, I have a question on how to align paired-end reads. In cases of very large fastq files, which make aligners like TopHat crash in a server with limited memory in RAM, I have seen people align one pair mate at a time, to prevent TopHat from crashing. I cann't come up with an argument against ...
paired-end written 6.2 years ago by GPR310 • updated 6.2 years ago by Farhat2.9k
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Comment: C: Gatk-2.3-9 And Input File Format
... Thanks so much. I have the RealignerTargetCreator running now in both BWA and TopHat2 alignments.The one thing I changed is to leave the ID=string option as default=1 in AddOrReplaceReadGroups.jar. That pretty much eliminated the recurring error: Read HWI-ST830:129:D1459ACXX:8:1208:6666:45578 is ...
written 6.2 years ago by GPR310

Latest awards to GPR

Popular Question 3.2 years ago, created a question with more than 1,000 views. For Retrieving Gene Names From 3'-End Aligned Reads
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Class_Code In Isoform-Fpkm-Tracking
Great Question 3.2 years ago, created a question with more than 5,000 views. For Problems With Chromosome Ordering When Running The Gatk Indelrealigner
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Gatk-2.3-9 And Input File Format
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Igvtools Index "Error: For Input String: "Pass""
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Scripture And Transcript Abundance
Popular Question 3.2 years ago, created a question with more than 1,000 views. For E-Box Promoters In Gene List
Epic Question 3.2 years ago, created a question with more than 10,000 views. For How To Split A Bam File By Chromosome
Appreciated 3.2 years ago, created a post with more than 5 votes. For How To Split A Bam File By Chromosome
Popular Question 3.2 years ago, created a question with more than 1,000 views. For How To Generate A Paired End File Suitable For Bwa
Prophet 3.2 years ago, created a post with more than 20 followers. For How To Split A Bam File By Chromosome
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Cuffdiff Very High/Low Ratios, Still Significant
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Defining Sart And End Boundaries In A Cufflinks Assembled Transcript
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Popular Question 3.2 years ago, created a question with more than 1,000 views. For Tophat2, Strand-Specific And Genes.Gtf
Popular Question 3.2 years ago, created a question with more than 1,000 views. For A-To-G Rna-Editing Vcf File Repository
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Bowtie Output "Not Enough Fields"
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Popular Question 4.0 years ago, created a question with more than 1,000 views. For Varscan2 Strandness Filter
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Class_Code In Isoform-Fpkm-Tracking
Epic Question 4.0 years ago, created a question with more than 10,000 views. For How To Split A Bam File By Chromosome
Great Question 4.0 years ago, created a question with more than 5,000 views. For How To Split A Bam File By Chromosome

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