User: Titus

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Titus310
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5 months, 1 week ago
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Posts by Titus

<prev • 75 results • page 1 of 8 • next >
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Comment: C: Are there downloadable DBs for hotspot mutations?
... may be you are looking for that : http://cancer.sanger.ac.uk/cosmic ...
written 1 day ago by Titus310
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Comment: C: Will the ordering of fasta references influence bwa mem alignment result?
... There is different result if you change number of threads because solution searched change. I'm not sure the order of the fasta change something at the end you still have same motif/reads. ...
written 3 days ago by Titus310
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Comment: C: Can IonProton sequencing data be processed using BWA + FreeBayes or CLC?
... Hi I use bwa on Ion torrent data and i have results ( in number of reads aligned ) quit similar to Iontorrent specific aligners. The problem is INDEL and homopolymer but it's not perfect with Iontorrent specific aligners. Best ...
written 7 weeks ago by Titus310
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Comment: C: GC content and average fold coverage of contigs
... Yes but if you are low %GC content you have low complexity sequence too (in an other word you are high %TA), that's also a problems for aligner/assembler. I'm sure to answer to your questions.... In you graph i don't know the normalization they use by species like number of reads per sequencing etc ...
written 7 weeks ago by Titus310
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Comment: C: GC content and average fold coverage of contigs
... Not sure to understand your question now :) can you give some details ? ...
written 7 weeks ago by Titus310
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Comment: C: GC content and average fold coverage of contigs
... Hi, That mean you are in low complexity genome zone and probably your assembler/aligner had difficulty merging contigs/reads :) Best ...
written 7 weeks ago by Titus310
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Comment: C: some problem about VCF produced by PICARD VARSCAN SOMATIC command
... I don't really understand the strand problem ? Can you give more details please /command ? ...
written 7 weeks ago by Titus310
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Comment: C: How can I transform CNV output data of Agilent 244K to TCGA/GDC data?
... Don't you have the "map" of the Chip and the corresponding coordinates ? In our case my colleagues use a software named CytoGenomic they give it a sort of bed but the probe names are not a single number. Maybe try to ask Myriad Genetics , i could be by anything without columns names :( I tried to ...
written 7 weeks ago by Titus310
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Comment: C: How to download SNPs from two SNP databases
... May be you can share your solution it could help someone else in the future :) ...
written 7 weeks ago by Titus310
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Comment: C: How can I transform CNV output data of Agilent 244K to TCGA/GDC data?
... Hi, May be the first columns is the reference of the probe , and the second the log ratio of the signal ? Best ...
written 7 weeks ago by Titus310

Latest awards to Titus

Supporter 3 days ago, voted at least 25 times.
Appreciated 9 weeks ago, created a post with more than 5 votes. For C: BWA: Why paired reads mapped to different chromosome?
Commentator 9 weeks ago, created a comment with at least 3 up-votes. For C: BWA: Why paired reads mapped to different chromosome?
Rising Star 11 weeks ago, created 50 posts within first three months of joining.
Scholar 3 months ago, created an answer that has been accepted. For C: finding homologs in human
Teacher 3 months ago, created an answer with at least 3 up-votes. For C: where to find a list of often mutated or lost regions in cancers
Scholar 4 months ago, created an answer that has been accepted. For C: finding homologs in human

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