User: lwc628
lwc628 • 200
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Posts by lwc628
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... The reason I am trying to avoid multiple alignment is because of this possible scenario. Suppose I have two contigs, and one contig shares the last 10% of its sequence with the first 10% of another contig. Multiple alignment would fail to stitch the two contigs....
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written 3.9 years ago by
lwc628 • 200
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... Let's say I have a set of short contigs(5 sequences) that I want to assemble into one contig.
I do not want to use multiple sequence alignment, but rather use a template sequence that will be used as a sort of hint.
If I align those 5 sequences against the template, I get a following coordinate f ...
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... I posted this question in the Trinity user group, and here is what Mr. Haas responded to my question:
###
I'm pretty sure that reads shorter than 25 will simply be ignored. I know they'll be ignored by the kmer counting step (initial part of Trinity), and pretty sure they'll be ignored later on by ...
written 4.3 years ago by
lwc628 • 200
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... I was curious if Trinity discard reads shorter than its default 25mer.
The reason why I asked is after quality checking and trimming, there are reads in my fastq files that are shorter than 25. I wanted to know what would happen to them in Trinity.
I assume they(reads shorter than 25 bases) would ...
written 4.3 years ago by
lwc628 • 200
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... Hi. I downloaded the M.mulatta genome release 73 and its associated annotations sometime ago.
Now Ensembl has the release 78, and there must be some updates, and I want to incorporate that into my new analysis.
Now the assembly hasn't changed(MMUL 1.0, Feb 2006), but I was wondering if I can use ...
written 4.4 years ago by
lwc628 • 200
• updated
4.4 years ago by
Devon Ryan ♦ 90k
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... Thanks for your comments. I generated a denovo transcriptome assembly using Trinity, and in it I have multiple isoforms for a gene model. Without reference, I don't know exon-exon junctions in those isoforms, which is why I asked this question.
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written 4.7 years ago by
lwc628 • 200
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... Aren't isoforms in the mRNA form made up of exons stitched together?
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written 4.7 years ago by
lwc628 • 200
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... Is there any program that detects the exon-exon junctures when provided with isoforms without using the genome reference sequence?
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written 4.7 years ago by
lwc628 • 200
• updated
4.7 years ago by
spiderdijon • 20
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...
One of my RNA seq reads have k mer content looking like below:
The reads have adapter trimmed. But I don't understand why there is a enrichment at the end of the reads. Has anybody seen this?
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written 4.7 years ago by
lwc628 • 200
• updated
4.7 years ago by
Istvan Albert ♦♦ 80k
4
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... I am stuck with the correlated and independent data combined in one study. Here's my dilemma:
Say X is a drug(explanatory variable) and Y is a gene expression(response variable).
Normally, you would give out drugs to a half of your group(randomly chosen) and placebo to the rest, measure the gene e ...
written 4.9 years ago by
lwc628 • 200
• updated
4.9 years ago by
karl.stamm ♦ 3.5k
Latest awards to lwc628
Scholar
4.3 years ago,
created an answer that has been accepted.
For A: Does trinity discard reads shorter than 25-mer?
Popular Question
4.5 years ago,
created a question with more than 1,000 views.
For Almost Nothing Mapped Using Bwa Or Bowtie. But A Lot Of Mapping In Blast
Popular Question
4.8 years ago,
created a question with more than 1,000 views.
For Almost Nothing Mapped Using Bwa Or Bowtie. But A Lot Of Mapping In Blast
Popular Question
4.9 years ago,
created a question with more than 1,000 views.
For How To Count The Reads Mapped To Exon And Exon-Exon Junctions?
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5.2 years ago,
voted at least 25 times.
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5.8 years ago,
created an answer with at least 3 up-votes.
For A: What Are Your Most-Used Public Data Repositories?
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