User: Gaffa

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Gaffa490
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Posts by Gaffa

<prev • 18 results • page 1 of 2 • next >
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Comment: C: How Can I Obtain Genome Scaffolds Using Paired End 454 Reads And An Hybrid Assem
... Just curious - why not MIRA? ...
written 7.8 years ago by Gaffa490
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Answer: A: Reads Per Contig From Sam File?
... As an alternative to samtools idxstats (answer given by Steve Lianoglou), Picard's BamIndexStats provides the same functionality. Example output: ``` chr1 length= 230218 Aligned= 52377 Unaligned= 1962 chr2 length= 813184 Aligned= 179139 Unaligned= 4749 chr3 length= 316620 Aligned= 7601 ...
written 8.0 years ago by Gaffa490 • updated 8 weeks ago by RamRS24k
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Comment: C: How Can Multiple Sage Tags Map To The Same Gene?
... could it be sequencing errors? ...
written 8.1 years ago by Gaffa490
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Comment: C: What Is The Most Conserved Protein In Metazoa?
... I can't point to any studies, but a good guess might be histones. ...
written 8.1 years ago by Gaffa490
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Comment: C: Snptest (Gen/Sample) Files To R
... It could be helpful if you posted a small example of what this file format looks like, and perhaps also what you want to convert it to ("so that they work in R" is not very specific - R is pretty flexible and does not require strictly specified file formats). ...
written 8.1 years ago by Gaffa490
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Comment: C: How To Best Deal With Adapter Contamination (Illumina)?
... That's true, but it's fairly easy to re-sync paired fastq files by going through the them and removing those reads that don't have a matching pair in the other file. ...
written 8.2 years ago by Gaffa490
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Comment: C: Insert Size Mean And Sd For Sanger Reads
... Do you have a reference genome against which these reads are/can be mapped? ...
written 8.2 years ago by Gaffa490
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Comment: C: Standard Genome Plus Vcf To Variant Genome
... See also: http://biostar.stackexchange.com/questions/6576/new-fasta-sequence-from-reference-fasta-and-variant-calls-file (GATK's FastaAlternateReferenceMaker as accepted answer) ...
written 8.3 years ago by Gaffa490
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Answer: A: Parse A Embl Like Format To Fasta Format
... This one-liner should do it: perl -ne 'if ($_ =~ /^ID (.+)/) { print ">$1" } elsif ($_ =~ /^P[TA] (.+)/) { print "; $1 " } elsif ($_ =~ /^\s{4}(.+)/) { print "\n$1\n" }' Output: >US74811111-0005 ; I-003, a gene and methods for its use ; NIX CORPORATION RESEARCH TRIANGLE PARK, NC MDNNPNI ...
written 8.5 years ago by Gaffa490
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Comment: C: How To Best Deal With Adapter Contamination (Illumina)?
... Thanks - I have now used this program with great success. ...
written 8.5 years ago by Gaffa490

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Prophet 7.6 years ago, created a post with more than 20 followers. For New Fasta Sequence From Reference Fasta And Variant Calls File?
Epic Question 7.6 years ago, created a question with more than 10,000 views. For How To Best Deal With Adapter Contamination (Illumina)?
Epic Question 7.6 years ago, created a question with more than 10,000 views. For New Fasta Sequence From Reference Fasta And Variant Calls File?
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Appreciated 8.7 years ago, created a post with more than 5 votes. For New Fasta Sequence From Reference Fasta And Variant Calls File?
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Appreciated 8.7 years ago, created a post with more than 5 votes. For A: Next Generation Read Sequence Assembly Visualization Software
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Teacher 8.7 years ago, created an answer with at least 3 up-votes. For A: Next Generation Read Sequence Assembly Visualization Software
Commentator 8.9 years ago, created a comment with at least 3 up-votes. For C: Plotting The Paradigm Shift Of Research Focus From Genomics To Metagenomics
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