User: genomics Newbie

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Posts by genomics Newbie

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Comment: C: Viewers for examining haplotypes
... Thank you for your reply! I have changed my original post from "all chromosomes" to only a specific few. Also, I have tried HaploView without success and Broad no longer supports the package. I think the genome viewers (i.e. IGV and UCSC genome viewer) might be useful? ...
written 7 days ago by genomics Newbie0
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Viewers for examining haplotypes
... Hello, What are some of the best software packages and viewers to examine haplotypes for a few specified chromosomes? Would IGV be appropriate? Generally are the input formats raw sequence files or can they be vcf files? I am trying to correlate this with ancestry. ...
haplotype chromosomes written 8 days ago by genomics Newbie0
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Variant Control Format (VCF) TO Mutation Annotation Format (.MAF)
... Is there an application which will accept a vcf as an input file and automatically prepare a .maf (mutation annotation format) for its output? I tried Ensemble's VEP application but could not save it in .maf format. Is the best alternative mskcc/vcf2maf ? Responses are appreciated! ...
vcf maf written 7 weeks ago by genomics Newbie0 • updated 7 weeks ago by adam.maikai430
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Comment: C: Finding adapters in sequences
... It looks like your response may be a comment. Can you create a response so that i can accept this as the answer? ...
written 12 weeks ago by genomics Newbie0
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Comment: C: Finding adapters in sequences
... Thank you for the speedy reply! Our sequences are 300 base pairs in length and we used paired-end reads sequenced with a MiSeq sequencer.. To confirm, if I remove the primers below I will automatically be removing the adapters? Can "primer" and "adapter" be used interchangably in documentation? ...
written 12 weeks ago by genomics Newbie0
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Finding adapters in sequences
... Hello, How do you know whether you have found all the adapters in your 16S sequences for removal? I know how to identify and remove the universal primers for our 16S V3-V4 regions (341 forward and 805 reverse) but do not know how to identify any adapters for removal. Adapters may be different tha ...
16s adapter written 12 weeks ago by genomics Newbie0 • updated 12 weeks ago by genomax49k
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Comment: C: [bwa sai2sam_pe] fail to locate the index
... Yes, I believe the path to the index is correct. The path points directly to the location where the hg19.amb, hg19.ann, etc. files are located. ...
written 3 months ago by genomics Newbie0
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[bwa sai2sam_pe] fail to locate the index
... I researched my two index error messages (1. [bwa_aln] fail to locate the index 2. [bwa sai2sam_pe] fail to locate the index) and am providing the following details for troubleshooting: : • Used the bwa indexing command…’bwa index -a bwtsw hg.fa -p hg’ o The indexes of hg19.amb, hg19.ann, hg19.bwt, ...
bwa index written 3 months ago by genomics Newbie0
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Comment: C: Creating a BWA index with an index_prefix
... Thank you for your reply! For this question I didn't see an accept button. ...
written 3 months ago by genomics Newbie0
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Comment: C: Creating a BWA index with an index_prefix
... Thank you. My command only generated the following indexes...hg19.sa, hg19.amb, hg19.ann hg19.bwt and hg19.pac. I did not see any hg19.fa index. Any ideas why the command did not generate the hg19.fa? ...
written 3 months ago by genomics Newbie0

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