User: Ambika
Ambika • 30
- Reputation:
- 30
- Status:
- New User
- Location:
- United States
- Last seen:
- 2 months, 3 weeks ago
- Joined:
- 2 years, 11 months ago
- Email:
- a***************@gmail.com
Posts by Ambika
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... Alex, thanks for the suggestion. will surely try this. ...
written 11 weeks ago by
Ambika • 30
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... Juke, I have a bam file generated from STAR alignment. I will use this file to see if its merged or not. Thanks!! ...
written 11 weeks ago by
Ambika • 30
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... JC, I have not done RT-PCR on my knocked strain, howeverr this is something I can do sooner. Thanks for the suggestion!!! ...
written 11 weeks ago by
Ambika • 30
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... Genomax, what about the fact that the 178 bp region does not have promoter sequence? Can we still consider the second part as a separate gene? ...
written 12 weeks ago by
Ambika • 30
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... Genomax,
I will look into this RACE assay, if it would help me distinguish the genes it would be great. Thanks ...
written 12 weeks ago by
Ambika • 30
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... Alex, blasted my gene in NCBI and found that in the closely related species and the size of the gene is around 1.6 Kb too. Interesting thing is that both genes predicted from funnotate have same PFAM domain. Because of this I thought may be there is gene duplication but they are not similar. ...
written 12 weeks ago by
Ambika • 30
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... JC,
I did RT-qPCR before to validate the gene expression and I designed my primers around the 3' end so it has the amplicon only from second gene. So, now to confirm do you think I need to design primer that could amplify the region from both genes? Thanks for the suggestion, I will look for the sp ...
written 12 weeks ago by
Ambika • 30
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5 follow
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... Hello everyone,
In this past couple of weeks I encountered a different problem which is giving me a lot of stress, I hope you can give me some suggestions. I did RNAseq analysis in a fungal species year ago using a genome file and genes predicted from AUGUSTUS ( which were generated by my lab membe ...
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... It is not a complete table I have some overlap regions more than 20kb as well. I do have the gene annotation file. Do you think comparing the protein sequences will help in distinguishing the accessory region of the genome. And thank you for suggesting that program I will look into that. ...
written 4 months ago by
Ambika • 30
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... Hello Biostars,
I am doing whole genome alignment using NUCmer (a program under MUMmer). I am using this alignment to separate core and accessory chromosome. From NUCmer alignment I generated delta files which I filtered using options -r and -g and generated the coordinate file. This coordinate fil ...
written 4 months ago by
Ambika • 30
Latest awards to Ambika
Centurion
12 weeks ago,
created 100 posts.
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3 months ago,
created a question with more than 1,000 views.
For Cuffmerge error while merging gtf files
Great Question
4 months ago,
created a question with more than 5,000 views.
For Feature Counts output interpretation
Great Question
9 months ago,
created a question with more than 5,000 views.
For Unable to access jarfile trimmomatic-0.35
Popular Question
9 months ago,
created a question with more than 1,000 views.
For Interpretation of Results from trimmomatic
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9 months ago,
created a question with more than 1,000 views.
For stranded vs not stranded Htseq-output differences
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9 months ago,
created a question with more than 1,000 views.
For HTseq error: Too few arguements
Popular Question
12 months ago,
created a question with more than 1,000 views.
For Cufflinks gtf file to htseq
Popular Question
12 months ago,
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For DESeq2 workflow for RNAseq
Supporter
13 months ago,
voted at least 25 times.
Popular Question
2.1 years ago,
created a question with more than 1,000 views.
For Deseq2 library load error
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created a question with more than 1,000 views.
For Unable to access jarfile trimmomatic-0.35
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created a question with more than 1,000 views.
For HTseq Pysam error
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2.1 years ago,
created a question with more than 1,000 views.
For Trimmomatic jar file
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2.1 years ago,
created a question with more than 1,000 views.
For Interpretation of Results from trimmomatic
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2.1 years ago,
created a question with more than 1,000 views.
For HTseq error: Too few arguements
Popular Question
2.1 years ago,
created a question with more than 1,000 views.
For DESeq2 workflow for RNAseq
Popular Question
2.1 years ago,
created a question with more than 1,000 views.
For Feature Counts output interpretation
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2.1 years ago,
created a question with more than 1,000 views.
For How to add column to a file from from another file having one common column but different number of rows
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2.3 years ago,
created a question with more than 1,000 views.
For Unable to access jarfile trimmomatic-0.35
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2.7 years ago,
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