User: abi

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abi280
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Posts by abi

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Comment: C: Repeat Regions In Rna-Seq Data
... That exactly is our problem - we have single end illumina reads. You are right on with having longer reads which could go into neighboring unique regions and hence be reported. Thanks anyways! ...
written 6.1 years ago by abi280
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Comment: C: Repeat Regions In Rna-Seq Data
... Thanks Josh for your response. OK I did overestimate the repeats in this bacterial genome compared to fungal and plant genomes although it is much more compared to other species like coli or salmonella. Here some background info on what we already have or did. The sequence of the organism is availab ...
written 6.1 years ago by abi280
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Repeat Regions In Rna-Seq Data
... Hi all, The genome of the bacterium that we work with is flooded with repeat regions. We are interested in one such repeat region which we believe might be transcribed. We have a RNA-seq data set in which we could look for this repeat. But the problem is that reads which map to such repeats would be ...
rna-seq written 6.1 years ago by abi280 • updated 6.1 years ago by swbarnes25.3k
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Comment: C: How To Calculate The Net Charge Of Amino Acids *Sequences/Peptides* At Ph 7 Usin
... I thought as well too that bionfo12 meant net charge of an peptide. Pathetic with poorly framed questions!! What is really sad is that there are people out here trying to help others out and in the end it turns out that it has been a waste of time for them just because of a poorly framed question!! ...
written 6.8 years ago by abi280
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Comment: C: Mycoplasma Cell Culture Contamination Affecting High-Throughput Data [Chip-Seq &
... I think there are 2 issues here. 1. Reads aligning to the genus mycoplasma. As can be seen here www.invivogen.com/docs/Insight200511.pdf, about 20 species of Mycoplasma could be associated with contaminated cell cultures. It might not be a problem to scan your reads against these genomes. And it is ...
written 6.8 years ago by abi280
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Answer: A: Extract Reads From A Bam File That Fall Within A Given Region
... Thanks guys, Actually the answer was there in Michael´s explanation in http://www.biostars.org/post/show/3407/how-to-extract-reads-from-bam-that-overlap-with-specific-regions/#3414 In his example, countOverlaps(genes, reads, type = "within") would do what I want. If type is within, the query interva ...
written 6.8 years ago by abi280
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Comment: C: Extract Reads From A Bam File That Fall Within A Given Region
... Yep Arun thats what I want and BTW, I do not have spliced reads! ...
written 6.8 years ago by abi280
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Comment: C: Extract Reads From A Bam File That Fall Within A Given Region
... I am sorry if I am confusing you guys. Lets say I have a 4 reads with the following start and end coordinates aligned on to the chromosome. start coordinates of the reads: 900, 1000, 1100, 1900 end coordinates of the reads: 1200, 1500,1700, 2300 My region of interest is 1000:2000 I want my outpu ...
written 6.8 years ago by abi280
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Comment: C: Extract Reads From A Bam File That Fall Within A Given Region
... Thanks Dk for your answer, in your example the output will be all reads starting anywhere between 18000-45500. What I want is to get out only the reads which also end in this region. For example starting at 18000 or higher and ending at 45500 or lower. Abi ...
written 6.8 years ago by abi280
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Extract Reads From A Bam File That Fall Within A Given Region
... Hi all This question could be considered as a follow up of this discussion. http://www.biostars.org/post/show/3407/how-to-extract-reads-from-bam-that-overlap-with-specific-regions/#3414 What I need is to extract reads from bam file that fall only within a given region (not overlap the given region) ...
bam written 6.8 years ago by abi280 • updated 11 months ago by Alex Reynolds28k

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