User: toralmanvar

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toralmanvar840
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Posts by toralmanvar

<prev • 177 results • page 1 of 18 • next >
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Comment: C: How to call and INDEL using GATK
... Please check the path you have specified for reference sequence. Error clearly tells that there is no reference fasta in the path provided. ...
written 8 weeks ago by toralmanvar840
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Comment: C: Convert .Gff3 File To 12-Column .Bed File
... Thank you Juke-34, PASA worked in our case. ...
written 8 weeks ago by toralmanvar840
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Comment: C: Convert .Gff3 File To 12-Column .Bed File
... Does AGAT script convert gff3 into 12 column bed? I want conversion in a way to get 12 column bed which can be used as an input for methykit. ...
written 8 weeks ago by toralmanvar840
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Answer: A: Convert .Gff3 File To 12-Column .Bed File
... Hello @t_pod, Did you got any solution to your problem? We are also using gff3ToGenePred for converting gff3 to genepred file but unfortunately getting output for only 2 chromosomes instead f 15. Any help is appreciated. ...
written 8 weeks ago by toralmanvar840
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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 7 months ago by toralmanvar840
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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 8 months ago by toralmanvar840
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Comment: C: Analysis of paired-end GBS data
... Have you got any solution to above mentioned problem? ...
written 11 months ago by toralmanvar840
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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 11 months ago by toralmanvar840
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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 11 months ago by toralmanvar840
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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 11 months ago by toralmanvar840

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