User: amnoronha1016

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Posts by amnoronha1016

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read orientation from library fragment
... I have been reading some literature on read orientation and unfortunately I am still confused about how read orientation relates to the original fragment. Let's say that the following is one strand of the library fragment. 5' P7 AAAAAATTTGGGGGGGGGGGG P5 3' From what I understand, before R1 is seq ...
next-gen sequencing written 10 weeks ago by amnoronha101640 • updated 4 weeks ago by Biostar ♦♦ 20
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Answer: A: 10x Supernova de novo assembly
... They've just come out with a technical note on smaller assemblies: https://support.10xgenomics.com/de-novo-assembly/sample-prep/doc/technical-note-guidelines-for-de-novo-assembly-of-genomes-smaller-than-~3-gb-using-10x-genomics-supernova-v12 ...
written 12 weeks ago by amnoronha101640
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Comment: C: Best statistical test for 1 vs 2 replicates
... thank you! i will have to put that in my repertoire. ...
written 4 months ago by amnoronha101640
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Comment: C: Best statistical test for 1 vs 2 replicates
... thanks! yes, it is RNA-seq. ...
written 4 months ago by amnoronha101640
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Best statistical test for 1 vs 2 replicates
... Hello all, I have to do a comparison of two groups. The first group has 1 sample and the second group has 2 samples. What is the most appropriate statistical test/software for this comparison? The resources that are most readily available to me are: 1. DeSeq2 2. Baggerly's test (test on proport ...
rna-seq written 4 months ago by amnoronha101640 • updated 4 months ago by h.mon8.7k
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Finding sequences of genome with structural variants.
... Hello, I have a bacterial reference genome and short sequencing reads from an organism belonging to the same species. I have already detected several structural variants in my sequenced sample and have a csv file for them (but not vcf). How do I get the exact sequence of the genome of this sequenc ...
sv assembly sequencing written 6 months ago by amnoronha101640
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Comment: C: Sequenced reads have high average Q30 but all the sequences are the same. How is
... Thank you, that trick will come in handy! ...
written 9 months ago by amnoronha101640
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Comment: C: Sequenced reads have high average Q30 but all the sequences are the same. How is
... Another thing to add is that we did check those sequences against the adapters--they did not match (unless the wrong adapters were communicated to me, but I'm going to try trimming with other adapters right now). It's good to know, though, that identical reads can produce high quality adapters. than ...
written 9 months ago by amnoronha101640
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Comment: C: Sequenced reads have high average Q30 but all the sequences are the same. How is
... This is not an amplicon experiment, it's transcriptome sequencing from human samples. We would not expect to get similar inserts. I think what happened is that the RNA extractions yielded very little RNA (not under my control) so we couldn't determine nucleotide diversity. It was also very difficult ...
written 9 months ago by amnoronha101640
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Sequenced reads have high average Q30 but all the sequences are the same. How is this possible?
... My HiSeq run yielded an average quality score of over Q35, with >90% of the bases being >Q30. Yet, when I analyze these reads, I can read the sequence right off the "nucleotide contributions" plot (this plot shows relative abundance of nucleotides at each base position in the read). Even if it ...
rna-seq hiseq written 9 months ago by amnoronha101640 • updated 9 months ago by harold.smith.tarheel3.8k

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