User: Bio_X2Y

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Bio_X2Y3.6k
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Posts by Bio_X2Y

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Comment: C: Ms/Ms Peptide Identification - Please Clarify "Monoisotopic Vs Average" Paramete
... Thanks John. I'm still unsure, however, what the parameter means in the context of Mascot/X!Tandem/etc, i.e. what are you "telling" Mascot when you choose "Monoisotopic". e.g. are you indicating that you are providing de-isotoped MS2 spectra where the monoisotopic means have been retained and the ot ...
written 6.9 years ago by Bio_X2Y3.6k
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Ms/Ms Peptide Identification - Please Clarify "Monoisotopic Vs Average" Parameter
... Both Mascot and X!Tandem offer a parameter for "monoisotopic vs average" (X!Tandem calls it "spectrum, fragment mass type"). Even after reading the documentation, I'm unclear on the meaning of this parameter - perhaps someone can clarify? In general, I understand the difference between MS1 and MS2 ...
mass-spec written 6.9 years ago by Bio_X2Y3.6k • updated 2.7 years ago by Biostar ♦♦ 20
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Rna-Seq: Difference In Read Quality Pattern Between Illumina Ga And Hiseq 2000?
... In the past, we've used an Illumina GA for our RNA-seq experiments. In general, we noticed that the reported quality of the read bases was highest at the 5' end of each read, and the quality dropped gradually towards the 3' end (as per the FASTQ files). This is what we expected. Recently, however, ...
illumina quality rna hiseq written 7.0 years ago by Bio_X2Y3.6k • updated 7.0 years ago by Brad Chapman9.2k
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Comment: C: How To Represent Multi-Mapping Paired-End Reads In Sam Format?
... I posted here to BioStar first, and cross-referenced this post on the mailing list. I would be tempted to leave it open here, and I'll update it with any relevant replies on the mailing list. ...
written 7.0 years ago by Bio_X2Y3.6k
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How To Represent Multi-Mapping Paired-End Reads In Sam Format?
... Imagine we have a read with two ends - A and B. An aligner finds that A maps uniquely to some location, and B can be mapped to two locations that satisfy the expected insert size. Conceptually, should we: Treat the ends as basically independent, and store 3 alignment records in SAM (A>P1, B> ...
paired rna sam multiple written 7.0 years ago by Bio_X2Y3.6k
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Comment: C: How To End Trim Sequences Using Prinseq?
... Perhaps the program can implement only one rule at a time? Maybe try running with "trim_qual_left", then run the output through the program again, the second time with "trim_qual_right"? ...
written 7.2 years ago by Bio_X2Y3.6k
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Comment: C: How To End Trim Sequences Using Prinseq?
... Perhaps you can only run one rule at a time? Maybe try running with "trim_qual_left", and then run it again for "trim_qual_right"? ...
written 7.2 years ago by Bio_X2Y3.6k
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Answer: A: How To End Trim Sequences Using Prinseq?
... I haven't used this program, but intuitively, I suspect the [?]trim_qual_left[?] and [?]trim_qual_right[?] work by clipping bases from each side until a base with quality 5 or higher is encountered. So you would end up with reads that might still contain low quality bases, but the two bases remainin ...
written 7.2 years ago by Bio_X2Y3.6k
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Answer: A: Ucsc/Ensembl Bam Converter?
... This feels like a risky thing to do. As Pablo points out, there are subtle differences between the two references (e.g. names of the unplaced and unlocalised contigs, masked PAR regions, etc.). Depending on your goals, these may or may not be important. Perhaps the trickiest difference is the mitoc ...
written 7.2 years ago by Bio_X2Y3.6k
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Comment: C: How Do I Transform A Binary Mass Spec File To Ascii Text Format
... I've never seen that format for machine-generated raw mass-spec data. Are you sure it's from a mass spec machine? This is a long shot, but perhaps the first few bytes of the file might be an ASCII representation of the generating instrument? ...
written 7.3 years ago by Bio_X2Y3.6k

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