User: vkkodali

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vkkodali2.4k
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Posts by vkkodali

<prev • 280 results • page 1 of 28 • next >
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Answer: C: Stringtie transcripts to Gene Name
... If I understand correctly, you don't see `GeneID:40027734` (which corresponds to the gene CJI97_002588 in the output of StringTie. RefSeq GFF3 files include several attributes in column 9, not all of which are copied over by StringTie. Using the RefSeq GFF3 as a starting point you can build a mappin ...
written 4 days ago by vkkodali2.4k
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Comment: C: Stringtie transcripts to Gene Name
... If you use a reference annotation file (`-G` parameter) at the time of transcript assembly using stringtie you should see the names from your reference GTF in the stringtie output. Only novel genes/transcript variants end up with the STRG identifiers. ...
written 5 days ago by vkkodali2.4k
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Answer: A: NCBI Genome Workbench tool
... No, NCBI Genome Workbench does not have this capability. You will need to use a variant caller (for example, `bcftools`) for this purpose. ...
written 19 days ago by vkkodali2.4k
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Answer: A: downloading full genbank file using Entrez efetch
... You need to use `rettype = 'gbwithparts'` to download the entire record. For more details, see [Table 1](https://www.ncbi.nlm.nih.gov/books/NBK25499/table/chapter4.T._valid_values_of__retmode_and/?report=objectonly) in the [EFetch documentation](https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4. ...
written 4 weeks ago by vkkodali2.4k
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Answer: A: Get corresponding Biosample accessions for very large list of SRA accesions?
... You can use [Entrez Direct](http://bit.ly/entrez-direct) for this as follows: $ esearch -db sra -query 'SRR5437876' | elink -target biosample | efetch 1: Human sample from Homo sapiens Identifiers: BioSample: SAMN06710536; Sample name: MCF-7; SRA: SRS2116118 Organism: Homo sapiens ...
written 4 weeks ago by vkkodali2.4k
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Comment: C: What kinds of gene ID types like below??
... Yes, these are all just transcripts assembled from reads. To find our which gene that is, you will have to align these transcripts (use the FASTA file from the GEO web link) to a reference genome for which an annotation exists. I think Trinity tutorial uses GMAP for alignments but you can probably u ...
written 5 weeks ago by vkkodali2.4k
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Answer: C: What kinds of gene ID types like below??
... These are Trinity transcript identifiers of the kind described [here](https://github.com/trinityrnaseq/trinityrnaseq/wiki/Output-of-Trinity-Assembly). The GEO link also has FASTA file with sequence data with the same identifiers: $ zgrep 'c100000_g1' GSE123550_Trinity.fasta.gz >c10000 ...
written 6 weeks ago by vkkodali2.4k
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Answer: A: Is there any tool/API available to convert GTF/GFF to JSON format?
... [NCBI Datasets](https://www.ncbi.nlm.nih.gov/datasets/) produces data report in json format that may contain all of the information you seek. You can download the [command line tool](https://www.ncbi.nlm.nih.gov/datasets/docs/command-line-start/) and try it out as follows: datasets download ge ...
written 6 weeks ago by vkkodali2.4k
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Comment: C: converting RefSeq Protein (NCBI) accession numbers to Gene Symbol
... I updated my answer now to show the protein accessions as well. Note, it adds additional columns to genes that encode >1 isoforms. ...
written 6 weeks ago by vkkodali2.4k
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Answer: A: Easiest way to homogenize gene aliases across datasets?
... You can use [NCBI Datasets](https://www.ncbi.nlm.nih.gov/datasets/) for this. Specifically, you can use the [command line tool](https://www.ncbi.nlm.nih.gov/datasets/docs/command-line-start/) as follows: for s in SELENOW SELW SEPW1 ; do echo -ne "$s\t" ; datasets summary gene symbol ...
written 6 weeks ago by vkkodali2.4k • updated 6 weeks ago by h.mon32k

Latest awards to vkkodali

Scholar 6 weeks ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 6 weeks ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
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Teacher 9 weeks ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
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Teacher 5 months ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
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Scholar 5 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 6 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Teacher 6 months ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 7 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
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Scholar 9 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 9 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
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Appreciated 11 months ago, created a post with more than 5 votes. For A: Obtain N50 stats from NCBI for all Hymenoptera genome assemblies
Scholar 12 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 12 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 13 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 13 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Good Answer 13 months ago, created an answer that was upvoted at least 5 times. For A: Obtain N50 stats from NCBI for all Hymenoptera genome assemblies
Appreciated 13 months ago, created a post with more than 5 votes. For A: Obtain N50 stats from NCBI for all Hymenoptera genome assemblies

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