User: Mainul

gravatar for Mainul
Mainul10
Reputation:
10
Status:
New User
Location:
Malaysia
Last seen:
2 weeks, 5 days ago
Joined:
3 years, 7 months ago
Email:
a************@gmail.com

Posts by Mainul

<prev • 11 results • page 1 of 2 • next >
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Comment: C: error while building database by snpEff
... So, to identify the heat shock gene I aligned weedy rice WGS sequences with MSUv6.1 reference genome [original alignment source][1] and finally create filtred SNP vcf file. So until SNP filtered there was no error. So once I did with variant calling further proceed to the SNP annotation by snpEff t ...
written 4 weeks ago by Mainul10
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(Closed) snpEff annotation error on rice sample aligned with MSUv6.1
... Is there anyone who did snpEff annotation with MSUv6.1 rice reference. Currently, I am working to identify the Heat shock gene from weedy rice. I have 9 WGS sequences which 5 belong to heat tolerance and 4 belong to heat susceptible. So, to identify the heat shock gene I aligned all those weedy ri ...
genome assembly sequence snp gene written 4 weeks ago by Mainul10
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Comment: C: error while building database by snpEff
... It was my first time to upload photos and code together, I will make sure in future to post in a proper way. Thanks for your help. Can you suggest to me which reference genome build should I have to take for MSUv6.1. `java -jar snpEff.jar build -gff3 -v MSU6v1` i tried this to build my own genome b ...
written 4 weeks ago by Mainul10
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Comment: C: How can i extract specific genes from WGS sequence.
... Thanks for your suggestion. I will work on it ...
written 4 weeks ago by Mainul10
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error while building database by snpEff
... I have 48 rice whole-genome sequences and I would like to do Analysis of the variants in the heat tolerance related genes and functional effects of non-synonymous SNPs. I already make assemble with MSUv6.1 (all.con) from http://rice.plantbiology.msu.edu/ and I have filtered vcf file. So now the prob ...
gene assembly snp software error written 4 weeks ago by Mainul10 • updated 4 weeks ago by RamRS27k
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How can i extract specific genes from WGS sequence.
... I have 48 rice whole-genome sequences and I would like to extract tolerant genes among them. I already make assemble with MSUv6.1 (all.con) from (http://rice.plantbiology.msu.edu/) and I have sorted.bam file. So now to extract tolerant gene what should I need to do further? If any expert suggested m ...
gene written 4 weeks ago by Mainul10
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Comment: C: How to use MSU7 rice genome as reference as there has fasta file format.
... Thanks, for your information. ...
written 8 weeks ago by Mainul10
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Comment: C: How to use MSU7 rice genome as reference as there has fasta file format.
... all.con is a complete genome sequence but is it a sequence to use alignment on BWA. as BWA only supports .fa file. ...
written 8 weeks ago by Mainul10
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How to use MSU7 rice genome as reference as there has fasta file format.
... I am working with Whole-genome sequence analysis. I have to use the MSU7 rice genome as a reference. Once I going to download reference seq from this site (http://rice.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/). I am not getting any fasta ...
genome assembly alignment written 8 weeks ago by Mainul10
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Comment: A: How to prove novel organism by sequencing
... So can I say it's novel based on blast result. Or should I go for more information analysis such as 1. Should I go with phylogenetic analysis to make it more accurate. 2. Dose have any experimental techie that proved novel species? ...
written 11 months ago by Mainul10

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