User: Frenkiboy

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Frenkiboy250
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Posts by Frenkiboy

<prev • 26 results • page 1 of 3 • next >
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Blastz score normalization
... Are the blastz scores normalized, by default, by the length of the corresponding query/target sequence? Thank you in advance. ...
blast written 3.3 years ago by Frenkiboy250
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Comment: C: Cufflinks Paired End Read Names
... It depends whether the read maps to one or multiple locations - if the aligner can determine the position of one read in a pair uniquely, but can't map the other one, I don't see why there would be a problem in using the one that mapped, especially since the reads are pretty long nowdays (>70bp). ...
written 7.2 years ago by Frenkiboy250
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Cufflinks Paired End Read Names
... Could you please tell me the proper way in which the read names need to be formatted in a bam file containing paired end reads, for the cufflinks to recognize them as paired end reads and not single reads? Do they need to have a proper suffix (e.g. _1/_2) or the names need to be the same? On a simi ...
rnaseq cufflinks written 7.2 years ago by Frenkiboy250 • updated 7.2 years ago by always_learning1.0k
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Merging Bam Files With Different Headers
... This might be a trivial question, but I would rather ask then make a mistake. What is the easiest way to merge two bam files that have different headers - the headers contain the same information regarding the chromosome names and lengths, but in one file they are sorted by char (eg. chr1 chr10), a ...
bam samtools written 7.4 years ago by Frenkiboy250 • updated 7.4 years ago by Devon Ryan96k
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Comment: C: How To Find Pseudogenes Of A Given Protein?
... Dear Khader, thank you so much for your answer, but I am already aware that I can find a list of all of the pseudogenes in a certain genome. Let me rephrase my question: given a gene (say Optn), is there an easy way to find its related pseudogenes? ...
written 7.5 years ago by Frenkiboy250
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Comment: C: How To Find Pseudogenes Of A Given Protein?
... pseudogene.org has outdated annotations - corresponding to the May 2004. genome built (unless I couldn't find the recent ones, which is highly plausible), and it requires 2 liftovers to get the coordinates to mm9 - mm10 ...
written 7.5 years ago by Frenkiboy250
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How To Find Pseudogenes Of A Given Protein?
... My question is rather trivial, Is there a resource which I can use to find pseudogenes of my favorite set of genes using only identifiers (not to have to use sequence comparison)? Best regards ...
written 7.5 years ago by Frenkiboy250 • updated 7.5 years ago by Emily_Ensembl21k
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Comment: C: Tags In Encode Rna Datasets
... I'm sorry to bother you, but in the reads you posted do not have the right flags. Correctly mapped paired end reads should have 2 sets of flags: 99 - 147 83 - 163 This link shows it in a nice way: http://ppotato.files.wordpress.com/2010/08/sam_output2.png ...
written 7.9 years ago by Frenkiboy250
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Tags In Encode Rna Datasets
... While playing around with the ENCODE RNA-seq data-sets, I noticed that some of the pair-end files have weirdly set flags. The following few lines are from the CSHL/wgEncodeCshlLongRnaSeqAdrenalAdult8wksAlnRep1.bam file. PAN_0073:1:69:16755:10476#0 163 chr1 3190766 255 76M = ...
seq encode rna written 7.9 years ago by Frenkiboy250 • updated 6.7 years ago by Biostar ♦♦ 20
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Comment: C: Mapping In Colorspace
... I have changed my question a bit. You are correct about the methodology. The thing that's been bugging me is that the reads in colorspace have multimap to many more locations. ...
written 8.0 years ago by Frenkiboy250

Latest awards to Frenkiboy

Great Question 2.8 years ago, created a question with more than 5,000 views. For How To Find Pseudogenes Of A Given Protein?
Popular Question 3.3 years ago, created a question with more than 1,000 views. For How To Find Pseudogenes Of A Given Protein?
Appreciated 7.2 years ago, created a post with more than 5 votes. For A: Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
Appreciated 7.2 years ago, created a post with more than 5 votes. For Encode Chipseq Peaks
Good Question 7.2 years ago, asked a question that was upvoted at least 5 times. For Encode Chipseq Peaks
Good Answer 7.2 years ago, created an answer that was upvoted at least 5 times. For A: Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
Popular Question 7.2 years ago, created a question with more than 1,000 views. For Strand In Pair-End Sequencing
Popular Question 7.2 years ago, created a question with more than 1,000 views. For How To Find Pseudogenes Of A Given Protein?
Popular Question 7.2 years ago, created a question with more than 1,000 views. For Mapping In Colorspace
Popular Question 7.2 years ago, created a question with more than 1,000 views. For Encode Chipseq Peaks
Popular Question 7.2 years ago, created a question with more than 1,000 views. For Cufflinks Paired End Read Names
Popular Question 7.2 years ago, created a question with more than 1,000 views. For Merging Bam Files With Different Headers
Popular Question 7.2 years ago, created a question with more than 1,000 views. For Chip Seq Pair End Data
Popular Question 7.2 years ago, created a question with more than 1,000 views. For Tags In Encode Rna Datasets
Teacher 7.2 years ago, created an answer with at least 3 up-votes. For A: Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
Teacher 7.2 years ago, created an answer with at least 3 up-votes. For A: Why Do Transcription Factors Bind To Intronic Regions Downstream Of The Transcri
Teacher 7.2 years ago, created an answer with at least 3 up-votes. For A: Synchronization Of Pair-End Reads
Student 7.2 years ago, asked a question with at least 3 up-votes. For Encode Chipseq Peaks

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