User: toralmanvar

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toralmanvar770
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Posts by toralmanvar

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Answer: A: Identify K value from ADMIXTURE cross-validation result
... According to me you can consider k=4:0.45242. ...
written 5 months ago by toralmanvar770
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News: Naxatra: Advance program on RNAseq and bioinformatics
... **For more details contact: bdgenomics.corp@xcelrislabs.com** ...
rnaseq ngs news handson workshop written 5 months ago by toralmanvar770
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Comment: C: bcl to fastq
... yes, you can download bcl2fastq from [here][1] and can install it offline. [1]: https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html ...
written 7 months ago by toralmanvar770
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Comment: C: ERROR MESSAGE: QD annotation at VariantRecalibrator
... Usually, in case of incompatibility of reference genome you end up with [this][1] kind of problems. But this not the case here. But give a try using reference genome from this [link][2] for 1000G VCF files. [1]: https://software.broadinstitute.org/gatk/documentation/article?id=11012 [2]: ftp:/ ...
written 7 months ago by toralmanvar770
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Comment: C: ERROR MESSAGE: QD annotation at VariantRecalibrator
... That's unusual. You might have gone through [this][1] GATK forum, but if not, see whether it can be useful to you. [1]: https://gatkforums.broadinstitute.org/gatk/discussion/8946/qd-annotation-not-found-variant-recalibrator-error ...
written 7 months ago by toralmanvar770
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Comment: C: how many files are generated after sorting of .bam file ?
... Check [this][1] [1]: https://www.biostars.org/p/289378/ ...
written 7 months ago by toralmanvar770
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Comment: C: ERROR MESSAGE: QD annotation at VariantRecalibrator
... Have you validated the input VCFs with ValidateVariants? ...
written 7 months ago by toralmanvar770
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Comment: C: The evidence of the gene annotation
... According to me, both can work as evidence. But in the case of blastx result, those are only annotated sequences which you consider, on the other hand latter gives you a complete set of proteins. ...
written 7 months ago by toralmanvar770
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Comment: C: Can I use VarScan for tumor_time2/tumor_time1 CNA and SNP calling?
... https://www.biostars.org/p/243387/ ...
written 7 months ago by toralmanvar770
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Comment: C: bcl to fastq
... Though it is not the proper solution. I think you can try taking undetermined reads left after demultiplexing of 3 samples as data for your 4 sample. If you have added PhiX Control then you can map undetermined reads to PhiX genome and can work with remaining data. ...
written 7 months ago by toralmanvar770

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Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How to extract specific rows based on row number from a file
Scholar 9 months ago, created an answer that has been accepted. For A: how to get the strand from a blast xml file
Scholar 11 months ago, created an answer that has been accepted. For A: how to get the strand from a blast xml file
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Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How to extract specific rows based on row number from a file
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