User: Davy

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Davy360
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Posts by Davy

<prev • 51 results • page 1 of 6 • next >
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Comment: C: Extracting Read Pairs From Region So That All Pairs Remain Intact
... Reads added above. Thanks for the assistance. ...
written 5.2 years ago by Davy360
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Comment: C: Extracting Read Pairs From Region So That All Pairs Remain Intact
... So I tried FixMateInformation, and that didn't work. I also tried (emphasis on tried) filtering with samtools view -f (tried 2 and 3 here) but I didn't really get anywhere. Samtools flagstat reports 0 singletons but picard now says "Found 2587 unpaired mates". Any other suggestions, let me know, bu ...
written 5.2 years ago by Davy360
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Comment: C: Extracting Read Pairs From Region So That All Pairs Remain Intact
... Thanks, but this gives the same result. ...
written 5.2 years ago by Davy360
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Extracting Read Pairs From Region So That All Pairs Remain Intact
... Hi all, I have some whole exome data and I am only interested in the exons of 4 genes, which I have in a bed file. I ,perhap naively, tried extracting only those reads using this bed file with samtools samtools view -b -L 4genes.bed myBAM.bam > myBAM.4genes.bam which works fine, except when I ...
fastq picard samtools bam written 5.2 years ago by Davy360 • updated 8 weeks ago by cmdcolin950
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Comment: C: Very High Percentage Of Reads Are Pcr Duplicates - Iontorrent
... Thanks Fabio and Arno. I will continue to seek opinions, but this does make sense to me, so I will continue on with the pipeline for now. Cheers! ...
written 5.3 years ago by Davy360
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Comment: C: Very High Percentage Of Reads Are Pcr Duplicates - Iontorrent
... Can you explain why I wouldn't need to remove the duplicates? If there is an error early on in the PCR cycle won't that propagate and cause spurious SNP detection, in addition to artificially inflating the read depth? ...
written 5.3 years ago by Davy360
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Comment: C: Very High Percentage Of Reads Are Pcr Duplicates - Iontorrent
... I used the standard bwa aln in version 0.6.2. The fastQC reports showed the tails of the reads to quite low quality, so I will try BWA-mem to see if the alignment quality improves. Cheers. ...
written 5.3 years ago by Davy360
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Comment: C: How Can I Find Specific Motifs Of Promoter Sequences Of A Large Number Of Genes
... Have you tried meme? http://meme.nbcr.net/meme/ ...
written 5.3 years ago by Davy360
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Very High Percentage Of Reads Are Pcr Duplicates - Iontorrent
... Hi All, Recently I have been given some targeted iontorrent sequencing data to play with. It's not large amount of data only ~ 18,000 unpaired reads. I have aligned the reads with BWA, pretty much the same as I have always done with illumina fastq files. (about 80% aligned, which seemed a bit low, b ...
sequencing samtools pcr written 5.3 years ago by Davy360
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Comment: C: Automated Literature Search For List Of Genes
... As usual, Pierre to the rescue!!! ...
written 5.5 years ago by Davy360

Latest awards to Davy

Great Question 5.2 years ago, created a question with more than 5,000 views. For Calculating Gc Content For All Ccds
Popular Question 5.2 years ago, created a question with more than 1,000 views. For Error In Bioperl Get Adaptor
Popular Question 5.2 years ago, created a question with more than 1,000 views. For Picard Samtofastq Only Extracts One Read, Then Throws An Error
Popular Question 5.2 years ago, created a question with more than 1,000 views. For Automated Literature Search For List Of Genes
Popular Question 5.2 years ago, created a question with more than 1,000 views. For What Are The It Requirements For High Throughput Sequence Analysis
Popular Question 5.2 years ago, created a question with more than 1,000 views. For Creating Hg19 Reference Index
Popular Question 5.2 years ago, created a question with more than 1,000 views. For Extracting Read Pairs From Region So That All Pairs Remain Intact
Popular Question 5.2 years ago, created a question with more than 1,000 views. For Calculating Gc Content For All Ccds
Student 5.2 years ago, asked a question with at least 3 up-votes. For Calculating Gc Content For All Ccds
Supporter 5.2 years ago, voted at least 25 times.
Commentator 6.4 years ago, created a comment with at least 3 up-votes. For C: Why Are There More Non-Synonymous Snps Than Synonymous Snps In The 1000 Genomes
Teacher 6.5 years ago, created an answer with at least 3 up-votes. For A: Microarray: How To Select One Of Multiple Probes Corresponding To A Gene
Popular Question 6.5 years ago, created a question with more than 1,000 views. For Calculating Gc Content For All Ccds

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