User: rohan

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rohan100
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Posts by rohan

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(Closed) Miseq loading with low concentration library
... Hi there, I have made a DNA library for miseq using truseq pcr-free dna HT kit (550bp insert). The problem is that at the end of library preparation and pooling, I need at least 2nM of library for denaturation. But I have only 1nM left in 10 ul. So I can not concentrate it more. (quantified by Kapa ...
truseq pcr-free dna denaturation miseq written 4.0 years ago by rohan100
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Answer: A: How to compute average depth of coverage for expression matrix
... 1] To sort bam file:  samtools sort file.bam file.sorted 2] Install and run bedtools to get coverage: coverageBed -d -abam file.sorted.bam -b /path/to/.bed/file/ref.bed > output.cov 3] This will include names to the columns of the output: (reference, start position, end position, base, covera ...
written 4.7 years ago by rohan100
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Comment: C: Using Pysam to extract paired reads
... There are known issues with insufficient documentation for pysam. If you are comfortable with perl, you can try Bio::DB::Sam instead. It will do the same job with enough documentation for troubleshooting. ...
written 4.7 years ago by rohan100
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Comment: C: Where Can I Find Fastq Data (Ngs Raw Data) And Published Results?
... I have a question. Since it is very related I chose to post it here.  Q: So when you say that you want to validate your analysis pipeline with published/publicaly available data. Do you get any rights to publish your results based on your analysis of somebody elses's data. What are the norms to use ...
written 4.7 years ago by rohan100
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Comment: C: Where Can I Find Fastq Data (Ngs Raw Data) And Published Results?
... Is there a SQLite interface for perl ? ...
written 4.7 years ago by rohan100
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Comment: C: Difference between 2D and Secondary structures
... i have mentioned the links in above answer.. but as you are new to "protein thing".. i think you can try reading the wikipedia article carefully.. its very comprehensive and will be very helpful all around.. for 2d structure there is no such a documentation that i could find.. as its just a method ...
written 4.7 years ago by rohan100
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Answer: A: Difference between 2D and Secondary structures
... In case of Secondary structures, its about alpha helix or beta sheets, more @ http://en.wikipedia.org/wiki/Protein_structure In case of 2D structures, its just a method of representation (visualization) of protein structure which is mainly aimed at inter-residue/strand contacts. more @ http://ww ...
written 4.7 years ago by rohan100
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Comment: C: Samtools Library Source Question -- Bam_Lpileup.C Vs Bam_Pileup.C
... i wonder how people aren't bothered about this.. description from Bio::DB::Sam.. "The Samtools library caps pileups at a set level, defaulting to 8000.  There is currently no way to specify an unlimited cap." This is outrageous..  by a cross check i luckily found the abnormal coverage(saturating ...
written 4.7 years ago by rohan100
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Comment: C: How To Retrieve Reads Supporting A Snp/Indel
... reg current version of sam2tsv (with quality scores).. is it there also difference in snp calling? because if i compare the outputs of both, the total number of lines is different. eg. test1.sam.sam2tsv1 test1.sam.sam2tsv2 are the outputs of current and previous versions resp.  kclabws1@kclabws1 ...
written 4.8 years ago by rohan100
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Comment: C: Get Amino Acid Changes From Snp Calls
... i have done sequencing of a single gene(600nts) carrying different amino acid mutations along the length of the gene.. i want to count the occurrence of mutations as depth per mutation.. how should i make the annotation file in this case? is snpeff applicable for this case? ...
written 4.8 years ago by rohan100

Latest awards to rohan

Teacher 4.7 years ago, created an answer with at least 3 up-votes. For A: Difference between 2D and Secondary structures
Student 4.7 years ago, asked a question with at least 3 up-votes. For How To Explain Uneven Coverage Of A Dna Seqment Obtained Via Pcr Amplification.

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