User: amnoronha1016
amnoronha1016 • 40
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Posts by amnoronha1016
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... 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 ...
written 10 weeks ago by
amnoronha1016 • 40
• updated
4 weeks ago by
Biostar ♦♦ 20
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... 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
amnoronha1016 • 40
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... thank you! i will have to put that in my repertoire. ...
written 4 months ago by
amnoronha1016 • 40
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... thanks! yes, it is RNA-seq. ...
written 4 months ago by
amnoronha1016 • 40
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... 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 ...
written 4 months ago by
amnoronha1016 • 40
• updated
4 months ago by
h.mon ♦ 8.7k
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... 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 ...
written 6 months ago by
amnoronha1016 • 40
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... Thank you, that trick will come in handy! ...
written 9 months ago by
amnoronha1016 • 40
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... 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
amnoronha1016 • 40
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... 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
amnoronha1016 • 40
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... 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 ...
written 9 months ago by
amnoronha1016 • 40
• updated
9 months ago by
harold.smith.tarheel • 3.8k
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