User: Titus

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Titus280
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Posts by Titus

<prev • 63 results • page 1 of 7 • next >
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Comment: C: Somatic Mutation Identification for Tumor without Normal
... You can have a look to gnomAD which is bigger and include ExAC : http://gnomad.broadinstitute.org/ . ...
written 3 days ago by Titus280
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Comment: C: pileup format: what's the difference between upper and lower case?
... Hi , Yes you understood rigth for reverse strand you read is reverse to align it , then it means c is g :) Yes you can sum all the c/C together because of complementarity of DNA. But for example if your gene is in reverse strand DNA and you want to know the translation of the protein consequences ...
written 6 days ago by Titus280
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Comment: C: Is it normal to have low expression levels of house keeping genes in plant RNA-s
... Hi , Did you check if you don't have some enrichment step in your experiment ? That's the random think in RNA-seq even if you compare with other result sometime you have bias unknown, even if you have same species with the same condition growth plant and the same experimental sequencing... Best ...
written 11 days ago by Titus280
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Comment: C: BWA: Why paired reads mapped to different chromosome?
... Hi , I m working in a cancer panel with 22 genes (something like 90 amplicons ) and i have same result as you and i think you have a bigger target then me. You should looks at the regions with MAPQ 0 an see a low complexity sequences. Best ...
written 11 days ago by Titus280
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Comment: C: BWA: Why paired reads mapped to different chromosome?
... Hi, other reasons are homologous/pseudo genes, or conserved domains Best Tristan ...
written 11 days ago by Titus280
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Comment: C: Variant calling using samtools
... Hey, What about this https://www.biostars.org/p/244044/ ? They said 50x faster than classic pipeline :) Best ...
written 15 days ago by Titus280
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Comment: C: How to map reads to tiny reference using bowtie2
... For the 2nd solution if you use 150 your bases length as references quality base will not be used during the mapping (only for the 20 bases if you have the quality base sequencing ). May be you can try to filter reads and keep only good quality 150 bases reads as references. About the 3th solution ...
written 16 days ago by Titus280
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Comment: C: How to map reads to tiny reference using bowtie2
... Hi, If i understood right you have 150 bases length reads and you want to map it against multiple ref of 20 bases length ? If it's that i can tell you i got the same problem but on bwa that you can't aligned read longer then ref if i remember correctly. The solutions which worked in this case were : ...
written 16 days ago by Titus280
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Comment: C: How to map the reads from a Bam file to another reference genome????
... Hi Cindy, If you have extract a fastq yes you can simply realign your reads against your new reference using bwa :) Best ...
written 17 days ago by Titus280
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Comment: C: Hotspot file to Ion torrent
... Hi, If you don't have a home made design you can find it like in the Thermo Fisher web site like : https://www.ampliseq.com/tmpl/view.action?tmplDesignId=48744395#/?listAction=tmplCoverageSummaryList&tmplDesignId=48744395&wrapperId=ajaxTableWrapper In this case you have to sign in to get ...
written 18 days ago by Titus280

Latest awards to Titus

Appreciated 10 days ago, created a post with more than 5 votes. For C: BWA: Why paired reads mapped to different chromosome?
Commentator 11 days ago, created a comment with at least 3 up-votes. For C: BWA: Why paired reads mapped to different chromosome?
Rising Star 22 days ago, created 50 posts within first three months of joining.
Scholar 8 weeks ago, created an answer that has been accepted. For C: finding homologs in human
Teacher 8 weeks 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 9 weeks ago, created an answer that has been accepted. For C: finding homologs in human

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