User: Puriney

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Puriney330
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330
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Trusted
Location:
New York City
Website:
http://puriney.github....
Last seen:
18 hours ago
Joined:
6 years, 6 months ago
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Use the Force, Read the Source

Posts by Puriney

<prev • 29 results • page 1 of 3 • next >
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Cuffdiff: All three conditions at once v.s. Pair-wise compare?
... I have RNA-seq data under three different environmental experiments with the goal to detect differently splicing transcripts. When dealing with my three conditions, let's cond_x, cond_y, cond_z, I could: Strategy 1: run cuffdiff with all of their alignments as inputs Strategy 2: pair-wise compar ...
cuffdiff written 4.4 years ago by Puriney330
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Answer: A: Tophat : How Many Reads Are Aligned ?
... #!/usr/bin/perl -w use strict; my $bam = shift; my $tmp = "/tmp/tmpNameList"; use List::Util qw(sum); `samtools view $bam | cut -f1 > $tmp`; `wc -l $tmp`; open NAMES, $tmp; my %hash; while (<NAMES>) { chomp; my $id = $_; $hash{$id} = 1; } my @values = values %hash; ...
written 4.8 years ago by Puriney330
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Comment: C: Is Tair10 Gbrowse 1-Based Or 0-Based?
... Oh, yeah. It makes sense. I need notice the resolution. Thanks for your quick reply~~~ ...
written 5.0 years ago by Puriney330
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Comment: C: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
... For god sake, check the TAIR10 Gbrowser http://tairvm17.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/ , it just like 0-based/1-based mixture to me (see post Help: TAIR10 GBrowser 1-based mixed with 0-based? ). Luckily we got IGV. (p.s. Plant research cannot triumph mammalian research, look at ucs ...
written 5.0 years ago by Puriney330
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Answer: A: How To Merge Isoforms For A Gene
... Probably you could take a look at https://gist.github.com/Puriney/6655074. Though better move is to get a BED12 finally rather than BED6. ...
written 5.1 years ago by Puriney330
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Comment: C: Samtools Tview Legend
... The strand info comes from the aligner. Aligner get input from genome.fasta file to build index, meanwhile the genome.fasta file is recorded in 5'->3' direction. Thus if the read matches the raw genome.fasta sequence, the read is considered mapped on the positive strand, and vice versa. I hope so ...
written 5.1 years ago by Puriney330
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Answer: A: Samtools Tview Legend
... I disagree with @Pierre. , : negative strand, . : positive strand. You could try to separate the reads by its strand using the bitwise flag. samtools -f 0x10 -b aln.bam> aln.neg.bam would give you all the reads mapped to negative strand, samtools -F 0x10 -b aln.bam>aln.pos.bam would ...
written 5.1 years ago by Puriney330
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Is Tair10 Gbrowse 1-Based Or 0-Based?
... TAIR10.org's GBrowser is 1-based or 0-based coordinate system? ! I am totally confused. For example, I want to have 3rd to 7th base: 3,4,5,6,7. All 5 bp. SAM, GFF are 1-based, thus [3, 7]. Clear. BAM, BED are 0-based, thus [2, 7). Make sense. The UCSC Genome Browser is uniformly displayed in ...
written 5.1 years ago by Puriney330 • updated 4.6 years ago by Chris Fields1.9k
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Answer: A: Tophat Library-Type : Illumina Truseq Stranded Total Rna Sample Prep Kit
... This could illustrate how to select your library-type if you really want to know why so. http://onetipperday.blogspot.com/2012/07/how-to-tell-which-library-type-to-use.html ...
written 5.1 years ago by Puriney330
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Comment: C: Is There Any Other Method For Isoform-Level Differential Expression Analysis Exc
... That document is quite impressive ...
written 5.7 years ago by Puriney330

Latest awards to Puriney

Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Reproduce Encode/Cshl Long Rna-Seq Data Visualization Viewed In Ucsc, But Failed
Good Question 2.1 years ago, asked a question that was upvoted at least 5 times. For Reproduce Encode/Cshl Long Rna-Seq Data Visualization Viewed In Ucsc, But Failed? [Done]
Student 3.8 years ago, asked a question with at least 3 up-votes. For Reproduce Encode/Cshl Long Rna-Seq Data Visualization Viewed In Ucsc, But Failed? [Done]
Good Question 4.6 years ago, asked a question that was upvoted at least 5 times. For Reproduce Encode/Cshl Long Rna-Seq Data Visualization Viewed In Ucsc, But Failed? [Done]
Popular Question 4.6 years ago, created a question with more than 1,000 views. For Intersectbed/Coveragebed -Split Purify Exon?
Supporter 4.6 years ago, voted at least 25 times.
Teacher 4.6 years ago, created an answer with at least 3 up-votes. For A: Reproduce Encode/Cshl Long Rna-Seq Data Visualization Viewed In Ucsc, But Failed
Student 4.6 years ago, asked a question with at least 3 up-votes. For Reproduce Encode/Cshl Long Rna-Seq Data Visualization Viewed In Ucsc, But Failed? [Done]

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