User: toralmanvar

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toralmanvar820
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Posts by toralmanvar

<prev • 173 results • page 1 of 18 • next >
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Comment: C: Tassel5v2 vcf file with 'N' in reference and alternate allele
... Thanks a ton Vijay for the reply. But this issue is related to plugin not able to use reference sequence to identify the adjacent base for obtained INDELs, in spite of providing reference genome in one of the parameters of DiscoverySNPCallerPluginV2. Though I got some help from the tassel goggle gro ...
written 3 days ago by toralmanvar820
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Tassel5v2 vcf file with 'N' in reference and alternate allele
... Hello All, Can anyone please help me understand why VCF file obtained using tassel5v2 pipeline "DiscooverySNPcallerV2" is giving 'N' in reference as well as alternate allele? When I check the particular position in reference there is no "N" in that particular position. Bowtie2 was used for tag mapp ...
tassel5v2 snpcalling gbs written 20 days ago by toralmanvar820
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Comment: C: Analysis of paired-end GBS data
... Have you got any solution to above mentioned problem? ...
written 3 months ago by toralmanvar820
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Comment: A: Maker Annotation pipeline Output error
... For us, it was possible to run MAKER only after reffering this [link][1] written by [darencard][2]. [1]: https://gist.github.com/darencard/bb1001ac1532dd4225b030cf0cd61ce2 [2]: https://gist.github.com/darencard He has explained each step in very nice manner. I think it will be useful to you ...
written 3 months ago by toralmanvar820
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Answer: A: Can I perform differential gene expression with samples from Poly-A and Ribo-dep
... If the aim of your study is to get differentially expressed mRNAs, then definitely you can compare both types of libraries as they both help enriching mRNA. But, if you are looking for expression analysis of specific non-coding RNAs then it would be difficult. ...
written 3 months ago by toralmanvar820
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Answer: A: number of cycles, Nextseq500, for whole exoems equencing, which option is more e
... I agree with [trauch][1]. But, mostly we sequence it using 2x150 bp chemistry and it gives good results. However, I think there is no reason of using 2x300bp chemistry for exome. [1]: https://www.biostars.org/u/18874/ ...
written 3 months ago by toralmanvar820
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Comment: C: Some Question About Converting sra format file to fastq format file
... Provide the command used, so that we can help you in better way. You can go through 4th post provided in this [link][1]. As your data is of oxford nanopore which is SE, you can try using –split-3, where you get all single end reads in separate file. [1]: https://sequencing.qcfail.com/articles/da ...
written 3 months ago by toralmanvar820
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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 9 months ago by toralmanvar820
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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 9 months ago by toralmanvar820
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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 11 months ago by toralmanvar820

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