User: Sparrow_kop

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Sparrow_kop180
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China
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2 weeks ago
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2 years, 6 months ago
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Posts by Sparrow_kop

<prev • 27 results • page 1 of 3 • next >
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Comment: C: Using GATK's HaplotypeCaller or Mutect2 for somatic cancer samples with no norma
... Hi, if you have only tumor sample and have to call somatic variant, then from my own experience Mutect2 is the best choice, and also I evaluated the performance between single sample and paired samples, I think single sample could also identify the positive somatic mutation but can not filter some i ...
written 3 months ago by Sparrow_kop180
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Answer: A: Retrieve amino acid sequences from old locusID?
... Hi, you can use R 'KEGGREST' library to extract the amino seq from the KEGG database: The below is the demo script: library(KEGGREST) library(Biostrings) aaseq_query <- keggGet("bpy:Bphyt_2906", "aaseq") aaseq <- as.character(unlist(aaseq)) aaseq [1] "MSEKEIDQVLV ...
written 3 months ago by Sparrow_kop180
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Answer: A: Retrieve amino acid sequences from old locusID?
... Hi, you can use R 'KEGGREST' library to extract the amino seq from the KEGG database: The below is the demo script: library(KEGGREST) library(Biostrings) aaseq_query <- keggGet("bpy:Bphyt_2906", "aaseq") aaseq <- as.character(unlist(aaseq)) aaseq [1] "MSEKEIDQVLV ...
written 3 months ago by Sparrow_kop180
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Comment: C: Calculate Radius of Gyration [python 3]
... Hi, maybe you can try PyMOL library. There is a python example to do this calculation: [Radius_of_gyration][1] [1]: https://pymolwiki.org/index.php/Radius_of_gyration ...
written 3 months ago by Sparrow_kop180
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Comment: C: RNA-seq read alignment
... You can remove "- c" option, and try again. From hisat2 help: "-c , , are sequences themselves, not files", but in your command , -1 and -2 refer to sequence file, not the sequence themselves.... "- c" can used in the below demo: hisat2 -c -x index -1 ATCTCGTCGTCGCT -2 ATGATGA ...
written 3 months ago by Sparrow_kop180
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Comment: C: TCGA data - GDC data portal vs. Firebrowse
... From the link [link][1], I think firebrowse will also do some filter. But almost will be retained. [1]: https://confluence.broadinstitute.org/display/GDAC/FAQ#FAQ-sampleTypesQWhatTCGAsampletypesareFirehosepipelinesexecutedupon ...
written 3 months ago by Sparrow_kop180
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Answer: A: TCGA data - GDC data portal vs. Firebrowse
... Hi, the data of Firebrowse is from the raw TCGA project, while on the GDC , they first produce some harmonization pipelines, which may filter out some data. From the [GDC FAQ][1] [1]: https://gdc.cancer.gov/about-gdc/gdc-faqs Which one ask: "Why are some harmonized data files missing?" Answe ...
written 3 months ago by Sparrow_kop180
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Comment: C: Processing barcoded sequencing data
... Hi, in fact you need not to know the random barcode sequence beforehand. It is a tag used to track and identify the raw dna fragment sequence. The figure below illustrate this under the hood. [the figure ][1] [1]: http://www.pnas.org/content/109/36/14508/F1.expansion.html Also , the question ' ...
written 3 months ago by Sparrow_kop180
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Answer: C: RNA-seq read alignment
... Could you post the commend line? Maybe some parameter is wrong. ...
written 3 months ago by Sparrow_kop180
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Comment: C: Differential gene expression between a RNA seq and microarray
... In my opinion, I think there are technology bias and bench effect to the two different kind of dataset. So maybe you could find DE gene in the two dataset separately, and then evaluate the overlapping DE genes. ...
written 3 months ago by Sparrow_kop180

Latest awards to Sparrow_kop

Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Gene annotation help
Scholar 5 months ago, created an answer that has been accepted. For A: Gene annotation help

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