User: MatthewP

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MatthewP60
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Posts by MatthewP

<prev • 45 results • page 1 of 5 • next >
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How to filter RNA editing data called by RED-ML
... Hello, everyone! I use [RED-ML][1] to analyse `RNA Editing` events in my `RNA Seq` data. The result data is simple: #P_edit: The probability of being a RNA editing site predicted by RED-ML #Chromosome Position Read_depth Reference Reference_support_reads Alternative ...
rna editing rna-seq written 17 days ago by MatthewP60
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Comment: C: snpEff for bacteria
... Hello Yair, I think it's better to describe how you do and paste your command(code). ...
written 18 days ago by MatthewP60
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Answer: A: web efetch Json out put which is not a real json
... Hello, you set `retmode=json` but this may not supported by `db=pubmed`, [this table][1] shows all default and valid `retmode` for `E-utilities` all databases. [1]: https://www.ncbi.nlm.nih.gov/books/NBK25499/table/chapter4.T._valid_values_of__retmode_and/?report=objectonly ...
written 18 days ago by MatthewP60
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Comment: C: Why rs193922900 and rs59736472 seem to be special for RNAEditor?
... Thanks finswimmer! I actually download ther newest version([release-95][1]) of dbSNP file. I go check the `vcf` file and find this two sites still in `vcf` file. 19 18786034 rs193922900 TGTC T.,T. . . dbSNP_151;TSA=sequence_alteration;E_Cited;AA=GTC 7 ...
written 19 days ago by MatthewP60
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Answer: A: VCF To FASTA
... Hello, [vcftools][1] has a command `vcf-consensus` which can convert `VCF` to `FASTA` file if you got the reference. Command like: cat ref.fa | vcf-consensus your_file.vcf.gz > out.fa [1]: https://github.com/vcftools/vcftools ...
written 20 days ago by MatthewP60
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Why rs193922900 and rs59736472 seem to be special for RNAEditor?
... Hello, everyone! I want to use [RNAEditor][1] . This need to prepare many database first, one of them is `VCF` for `dbSNP`. This is the command given by [document][2]. wget -qO- ftp://ftp.ensembl.org/pub/release-83/variation/vcf/homo_sapiens/Homo_sapiens.vcf.gz |gunzip -c |awk 'BEGIN{FS="\t";OF ...
rna-seq snp rnaeditor written 20 days ago by MatthewP60
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Comment: C: Tools To Do the Alternative Splicing Analysis
... Hello, [rMATS][1] is a tool i am using, you can have a look. [1]: http://rnaseq-mats.sourceforge.net/ ...
written 24 days ago by MatthewP60
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Answer: A: How to convert data from NCBI E-utilities.efetch to python data object?
... Hello, I find `E-utils` can return `xml` if you set `retmode=xml`. Example: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=79669,10059,23548,8999&retmode=xml Here is all support `retmode` list: https://www.ncbi.nlm.nih.gov/books/NBK25499/table/chapter4.T._valid_va ...
written 25 days ago by MatthewP60
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How to convert data from NCBI E-utilities.efetch to python data object?
... Hello, everyone! I want to use [E-utilities][1] to get all gene information. I already get all gene UIDs and next step is use `E-utils.efetch` get gene record. However I find it's hard to extract informations I need from the `E-utils.efetch` return data. Here is one example link getting gene records ...
ncbi python written 28 days ago by MatthewP60
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What is the best way to get all human genes(name/UID) ?
... Hello, I want to get gene summary for **all human genes** by using [The Entrez Programming Utilities (E-utilities)][1] provided by NCBI. First of all I need to get the set of human genes name(seems gene don't have UID?), I think I can get that from `GTF` file. But I hope there is better way. Thanks ...
gene ncbi written 4 weeks ago by MatthewP60

Latest awards to MatthewP

Scholar 25 days ago, created an answer that has been accepted. For A: How to convert data from NCBI E-utilities.efetch to python data object?
Supporter 25 days ago, voted at least 25 times.

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