User: mks002

gravatar for mks002
mks002190
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190
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Location:
Bangalore. India
Website:
http://www.manishkumar...
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Posts by mks002

<prev • 91 results • page 1 of 10 • next >
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Comment: C: MAKER command maker2zff .ann and .dna files are empty
... Hi, Check the alternative which I've given in this thread. ...
written 3 months ago by mks002190
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Answer: C: GO enrichment analysis graphs after goseq: any easy solutions?
... Hello, Hope you find the following tools useful in your work. For making Bar Plot for publication, it can be done using [GraphPad][1] tool. For Making Enrichment Plot, u can use R package [clusterProfiler][2]. Biological Network can be done using Cyctoscape App [clueGo][3]. [1]: https://www. ...
written 6 months ago by mks002190
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Comment: C: Some Question About Converting sra format file to fastq format file
... I think nanopore sequencing data does not have any quality score. Fastq has a quality score. So you can get fast5 file out of SRA check the link [how-to-get-nanopore-minion-fast5-from-sra][1]. Later u can use [poretools][2] to convert fast5 to fastq. [1]: https://bioinformatics.stackexchange.com ...
written 8 months ago by mks002190
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Comment: C: Seeking Freelance bioinformatician
... 'manishkumarsinha002 [AT] gmail [dot] com' I would be helpful, So you can write to me. ...
written 9 months ago by mks002190
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Answer: C: How to find if a rsID is exomic ?
... Check the link [EVA][1] [1]: https://www.ebi.ac.uk/eva/ ...
written 9 months ago by mks002190
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Comment: C: Relaxed alignment using Bowtie
... Your calculation is right for 4 %. You must be knowing the default seed length ( -l ) is 28. But if give it 75, Reads of smaller length will be not be mapped (I think). Since your read chemistry is 1*75 and u must carry trimming and many of your read lengths would have become shorter due to quality ...
written 9 months ago by mks002190
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Comment: C: How to better find and select the appropriate data set for my research?
... You can have look at [Encode][1] . Hope this helps you out. [1]: https://www.encodeproject.org/ ...
written 11 months ago by mks002190
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Comment: C: Map genes to the ids
... You can try out [g:Profiler][1]. Hope this would solve your query. [1]: https://biit.cs.ut.ee/gprofiler/convert ...
written 11 months ago by mks002190
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Comment: C: How to find read count for a newly discovered transcript
... For mapping you can use Hisat program and then you use Depth of coverage under GATK program . By this exactly u can know about the coverage for the particular transcripts. -L option u check while running the GATK program where you can provide your interest of transcript in bed format (so for particu ...
written 11 months ago by mks002190
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Comment: C: What to do after differential expression
... RNA-Seq variant analysis you can perform apart from annotating the DEGs and performing enrichment analysis. ...
written 11 months ago by mks002190

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Popular Question 7 months ago, created a question with more than 1,000 views. For Methylation Analysis (Bisulfite sequencing)
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Popular Question 17 months ago, created a question with more than 1,000 views. For MAKER command maker2zff .ann and .dna files are empty
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Popular Question 19 months ago, created a question with more than 1,000 views. For MAKER command maker2zff .ann and .dna files are empty

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