User: kmcarr00

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kmcarr00270
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4 years ago
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Posts by kmcarr00

<prev • 14 results • page 1 of 2 • next >
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Answer: A: DNA de-novo assembly for plants different than rest organisms?
... The data set you are trying to assemble (http://www.ncbi.nlm.nih.gov/sra/SRR1045129) is transcriptomic (RNA-Seq) data. You can not use this data for genome assembly. ...
written 4.3 years ago by kmcarr00270
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Answer: A: What does the @HD GO record type mean in a BAM file?
... Looking back at historical SAM spec documents it appears that the @HD GO: tag was removed in the transition from v1.2 to v1.3 of the file format. Obviously your earlier file (VN:1.0) predates this change and your recent one (VN:1.4) comes after. The GO tag stood for "Group Order" and apparently had ...
written 4.3 years ago by kmcarr00270
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Comment: C: Roche 454: How to know if reads are paired ?
... You are right Lex. It has been so long since I've dealt with 454 data I forgot about that format. ...
written 4.5 years ago by kmcarr00270
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Answer: A: Roche 454: How to know if reads are paired ?
... In 454 technology there is no such thing as paired reads, at least in the sense that we all understand paired end sequencing. Given the design of their bead based sequencing it is impossible to generate reads from both ends of a template fragment. All 454 reads single reads, possibly with a barcode ...
written 4.5 years ago by kmcarr00270
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Comment: C: Using Trinity with case/control data
... You can provide a list of file names for the --left and --right command line parameters but that list of names should be a comma separated list, not space separated. I fear that in this case Trinity may have taken the first file in each list and ignored the rest. ...
written 4.5 years ago by kmcarr00270
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Answer: A: Paired-end 454 data - forward run consisting only of TCAG
... TCAG is the "key" sequence at the beginning of every 454 library molecule (they did change the sequence to distinguish FLX from FLX Titanium). The sequencer uses this key to one, identify library beads as opposed to control beads which have different key sequence and two, calibrate the signal intens ...
written 4.5 years ago by kmcarr00270
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Comment: C: How To Randomly Sample A Subset Of Lines From A Bed File
... But this is not a single random sampling. If the OP wants to subset 10,000 lines then he is performing 10,000 random samplings out of the original population without replacement. Assuming a good distribution of reads across chromosomes in the original population (BED file) the probability of samplin ...
written 5.3 years ago by kmcarr00270
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Answer: A: Genbank Multiple Cds For One Gene
... Martijn's answer showed a great example of how GenBank records report multiple transcripts and protein products but there is a very important gotcha to be aware of. There is NO explicit or implicit association made between a CDS entry and its corresponding mRNA. The CDS feature entry contains no mRN ...
written 5.9 years ago by kmcarr00270
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Comment: C: Have Anyone Done Bacterial Transcriptomics Using Miseq?
... The OP is asking about RNA-Seq. Coverage, per se, is not the driving consideration for RNA-Seq, read counts are. The MiSeq can generate ~15x10^6 reads (or read pairs) in one run. For a complex eukaryote that number is _barely_ enough for one replicate. For a bacterium with a simpler transcriptome my ...
written 5.9 years ago by kmcarr00270
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Answer: A: How Convert The Protein Sequence Coordinates To Exon Sequence Coordinates(Or Vic
... I have worked with Bio::Coordinate::GeneMapper once in the past and I found there were a couple of "gotchas" (I won't call them bugs, but....). In my use case I had SNP locations identified by NGS and wanted to determine what, if any, amino acid substitutions these would cause, so I had to map from ...
written 5.9 years ago by kmcarr00270

Latest awards to kmcarr00

Scholar 4.3 years ago, created an answer that has been accepted. For A: DNA de-novo assembly for plants different than rest organisms?
Appreciated 4.3 years ago, created a post with more than 5 votes. For C: Removing Duplicates From Rna-Seq Data
Teacher 4.3 years ago, created an answer with at least 3 up-votes. For A: What does the @HD GO record type mean in a BAM file?
Appreciated 5.2 years ago, created a post with more than 5 votes. For C: Removing Duplicates From Rna-Seq Data
Commentator 5.2 years ago, created a comment with at least 3 up-votes. For C: Removing Duplicates From Rna-Seq Data

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