User: Lisa Ha

gravatar for Lisa Ha
Lisa Ha50
Reputation:
50
Status:
New User
Location:
Germany
Last seen:
2 months, 3 weeks ago
Joined:
3 years, 2 months ago
Email:
l***********@gmail.com

Posts by Lisa Ha

<prev • 7 results • page 1 of 1 • next >
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Answer: A: can variants be called between two genomes?
... You could simulate reads from one of the genomes using [wgsim][1] and then use a normal pipeline to call the variants. As an alternative, there is a tool called [LAST][2] that was built specifically for a genome-genome comparison (I have never used this, though). [1]: https://github.com/lh3/wgs ...
written 5 months ago by Lisa Ha50
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Answer: A: How can I analyze more than two conditions in DESeq2?
... You can definitely use DESeq2 for that. The vignette even has a section on different ways of analysing time-series data with DESeq2. [DESeq2 vignette][1]. Which approach you use depends on your biological question though, which isn't clear from your question. You can also find an example workflow [h ...
written 5 months ago by Lisa Ha50
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Comment: C: How to get plasmid or costruct sequence from fastq file in c.elegans Whole-genom
... I doubt there is a single tool that does exactly what you want. You're going to have to put in a bit of effort. You can use grep on the command line to extract the reads that contain parts of your construct. Then map these to the genome and look at where the reads align (and stop aligning) with a ge ...
written 5 months ago by Lisa Ha50
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Answer: A: How to get plasmid or costruct sequence from fastq file in c.elegans Whole-genom
... You can get the flanking sequences by extracting the reads that contain the beginning or end of the construct. Then you can search for the flanking sequences in the genome. To verify the position, you can do a PCR on the strain containing the construct. ...
written 5 months ago by Lisa Ha50
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Answer: A: script for task or AWK
... That was a nice monday morning challenge for working on my python skills. The max value for the first sequence is different from your answer template, but consistent with the actual values in file2. import csv # open both files and store sequences from file1 as list stream = open("file ...
written 6 months ago by Lisa Ha50
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Answer: A: Conclusions to draw from PCA analysis regarding mapping
... Thank you, Devon. I will double-check the differently aligned reads to see what I can make of it. So you don't see a problem with using blat on short reads? ...
written 3.2 years ago by Lisa Ha50
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Conclusions to draw from PCA analysis regarding mapping
... Hey everyone, I have performed a RNAseq experiment with two closely related species, for one of which I have an assembled transcriptome from previous sequencing. I tried various options for mapping both species to the existing transcriptome, once with CLC Genomics Workbench with looser parameters f ...
R rna-seq written 3.2 years ago by Lisa Ha50

Latest awards to Lisa Ha

Scholar 6 months ago, created an answer that has been accepted. For A: script for task or AWK
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Conclusions to draw from PCA analysis regarding mapping

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