User: Chris Penkett

gravatar for Chris Penkett
Chris Penkett480
Reputation:
480
Status:
New User
Location:
Cambridge, UK
Website:
http://biostar.stackex...
Last seen:
6 years, 10 months ago
Joined:
8 years, 8 months ago
Email:
c************@yahoo.com

Posts by Chris Penkett

<prev • 47 results • page 2 of 5 • next >
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Answer: A: Gene Expression Analysis - Microarrays - Geneset
... If you don't want to start with BioConductor, and want something with a GUI you could try MeV and/or TM4 or GeneSpring - the latter is commercial and requires a license. ...
written 7.5 years ago by Chris Penkett480
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Comment: C: Microarray Statistics
... Are you using illumina array or sequence data? ...
written 7.5 years ago by Chris Penkett480
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Comment: C: Using Genes List From Limma Venn Diagram To Make Heat Map
... Looks like your Venn diagram code is all on one line, which is hard to read. ...
written 7.5 years ago by Chris Penkett480
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Answer: A: Bwa Seed Length
... There is a page here about using BWA (and other aligners) to map simulated reads by the author of BWA, the simulated reads he uses are 100 bp and he uses the default BWA parameters. The simulated reads won't have the same error characteristics as illumina reads for example, but probably most people ...
written 7.5 years ago by Chris Penkett480
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Comment: C: Differing Bwa Mapq Scores For A Read Depending On How I Build The Transcriptome
... The name of the paired match is different for the poorer score - maybe it thinks it's on a different chromosome? ...
written 7.5 years ago by Chris Penkett480
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Answer: A: Trim The Low-Quality End Of 100Bp Read
... This is too long to add as a comment. To convert fastQ files, I have an alias in my bash startup file (.bashrc): % grep ill2sanger .bash_aliases alias ill2sanger="perl -lpe 'BEGIN {\$count = 0} chomp; tr/\x40-\xff\x00-\x3f/\x21-\xe0\x21/ if \$count++ % 4 == 3'" Run it like this: % ill2sanger tmp.f ...
written 7.5 years ago by Chris Penkett480
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Comment: C: Trim The Low-Quality End Of 100Bp Read
... bwa aln -I should work: % bwa aln 2>&1 | grep "-I" -I the input is in the Illumina 1.3+ FASTQ-like format ...
written 7.5 years ago by Chris Penkett480
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Comment: C: Bowtie/Tophat With Fasta Converted From Fastq In Qc With Fastx ?
... Bowtie takes fasta files with the -f option. ...
written 7.5 years ago by Chris Penkett480
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Answer: A: Trim The Low-Quality End Of 100Bp Read
... Use the -q flag in bwa aln to trim reads below that Q score according to From the manual page: -q INT Parameter for read trimming. BWA trims a read down to argmax_x{\sum_{i=x+1}^l(INT-q_i)} if q_l<INT where l is the original read length. [0] There is also the SolexaQA and prinseq packages that ...
written 7.5 years ago by Chris Penkett480
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Comment: C: Changing Bowtie Settings In Tophat?
... In RNA-seq - it seems to be quite common that short reads do map more than once. With the default -g of 40, it will only throw away highly repeated sequences, so some people use a -g of 10. ...
written 7.5 years ago by Chris Penkett480

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