User: alpha2zee

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alpha2zee100
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Posts by alpha2zee

<prev • 12 results • page 1 of 2 • next >
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Answer: A: Both Paired And Unpaired Read Data Input For Subread Rna Sequencing Read Alignme
... Subread, as of version 1.4.3-p1, does not accept both paired and unpaired data for the same sample... see https://groups.google.com/forum/#!topic/subread/3tkBGjz6zVI ...
written 6.1 years ago by alpha2zee100
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Answer: A: Poor Quaility Rna-Seq Data
... You should also consider the expertise of those who mapped the read data. Is it possible that mapping wasn't done properly... for instance, would removal of poor quality trailing bases from the reads, contaminating adapter sequences, etc. have improved the mapping? ...
written 6.1 years ago by alpha2zee100
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Both Paired And Unpaired Read Data Input For Subread Rna Sequencing Read Alignment
... Does anyone know if the Subread RNA seq. aligner software accepts both paired and unpaired read data-files for the same sample, the way Tophat does? The Subread manual doesn't say anything on this. In my tests, Subread doesn't accept comma-separated paired and unpaired file-names (Tophat's usage), ...
alignment rna-seq written 6.1 years ago by alpha2zee100
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Comment: C: Samtools Mpileup And Overlapping Paired-End Reads
... Thanks. I had a similar response to my cross-post, at http://seqanswers.com/forums/showpost.php?p=123101&postcount=4. The poster suggested clipping overlapping mates with, among other tools, bamUtil/clipOverlap. ...
written 6.2 years ago by alpha2zee100
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Comment: C: Samtools Mpileup And Overlapping Paired-End Reads
... Sorry, is cross-posting a no-no? I am trying to reach more people and plan to post here a link to any conclusive answer I get elsewhere. ...
written 6.2 years ago by alpha2zee100
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Samtools Mpileup And Overlapping Paired-End Reads
... I am using samtools mpileup to generate a pileup for paired-end RNA sequencing data. I am curious about how samtools handles pair mates whose read mappings overlap. With regard to the simple example below, for positions 7-11, are both pair mates enumerated? position 1 6 11 16 reference ...
paired-end pileup rna-seq written 6.2 years ago by alpha2zee100 • updated 2.2 years ago by Owen S.350
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Differences Between Reference Human Genome Assemblies From Different Sources
... I am relatively new to analysis of whole transcriptome RNA sequencing data. I am planning to map human RNA sequencing reads against the reference human genome/transcriptome (i.e., generate BAM files from fastq files). I notice that reference genome assemblies are available from a number of sources: ...
rna-seq written 6.2 years ago by alpha2zee100 • updated 12 weeks ago by MatthewP390
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Answer: A: Looking For Frequency Of A Very Specific Rna Editing Event In Publicly Available
... Thank you for the suggestions. I was able to use samtools mpileup and a Python script for my analyses. ...
written 6.7 years ago by alpha2zee100
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Looking For Frequency Of A Very Specific Rna Editing Event In Publicly Available Rna-Seq Data
... I am working on a ubiquitously and well expressed gene whose ~1.5 kb-sized transcripts get mutated at one and only one site. The mutation is a nonsense one that changes an ORF codon of the mRNA to a stop codon. The underlying biology and whether this mutation occurs in all or specific cells is unkno ...
rna tcga mutation blast sequencing written 6.7 years ago by alpha2zee100
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Answer: A: Combining Illumina Ga And Hiseq Microrna Sequencing Data-Sets
... Various analyses that I recently perform suggest that the data can indeed be combined. As I mentioned, I have two different data-sets ('GA' and 'HiSeq'). For assessing the feasibility of combining the data, I start with data-sets of absolute count values. Within each data-set, the count values are ...
written 6.9 years ago by alpha2zee100

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