User: lwc628

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lwc628200
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3 years, 10 months ago
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6 years, 7 months ago
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Posts by lwc628

<prev • 26 results • page 1 of 3 • next >
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Comment: C: What program do I use to generate a single contig given a set of short contigs a
... 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.... ...
written 3.9 years ago by lwc628200
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What program do I use to generate a single contig given a set of short contigs and the template?
... 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 ...
assembly sequence alignment written 3.9 years ago by lwc628200 • updated 3.9 years ago by h.mon25k
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Answer: A: Does trinity discard reads shorter than 25-mer?
... 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 lwc628200
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Does trinity discard reads shorter than 25-mer?
... 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 ...
trinity rna-seq denovo assembly written 4.3 years ago by lwc628200
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Can I download ENSEMBL gtf whose release number is different from that of the corresponding genome as long as the assembly is identical?
... 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 ...
genome annotation ensembl written 4.4 years ago by lwc628200 • updated 4.4 years ago by Devon Ryan90k
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Comment: C: Without genome reference, how to find exon-exon junctions given isoforms
... 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. ...
written 4.7 years ago by lwc628200
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Comment: C: Without genome reference, how to find exon-exon juncture given isoforms
... Aren't isoforms in the mRNA form made up of exons stitched together? ...
written 4.7 years ago by lwc628200
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Without genome reference, how to find exon-exon junctions given isoforms
... Is there any program that detects the exon-exon junctures when provided with isoforms without using the genome reference sequence?   ...
rna-seq written 4.7 years ago by lwc628200 • updated 4.7 years ago by spiderdijon20
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Explanation for strange kmer enrichment at the end of the RNA-seq reads
...   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?   ...
rna-seq written 4.7 years ago by lwc628200 • updated 4.7 years ago by Istvan Albert ♦♦ 80k
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How to account for between-subjects variability in this particular RNA-seq study?
... 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 ...
rna-seq written 4.9 years ago by lwc628200 • updated 4.9 years ago by karl.stamm3.5k

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?
Supporter 5.2 years ago, voted at least 25 times.
Teacher 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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