User: vkkodali

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vkkodali1.1k
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Posts by vkkodali

<prev • 116 results • page 1 of 12 • next >
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Answer: A: Annotate CpG Islands for a new genome
... See: https://www.biostars.org/p/349994/#350026 ...
written 8 days ago by vkkodali1.1k
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Comment: C: How can i extract FPKM from my GTF file which is created by stringtie?
... Assuming that your GTF file is same as above, you can do the following: $ grep 'TPM' temp.txt | cut -f9 | sed -r 's/.*transcript_id "([^"]*).*TPM "([^"]*).*/\1\t\2/g' | sed '1i#transcript_id\tTPM' ...
written 8 days ago by vkkodali1.1k
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Comment: C: Entrez Direct problems
... Thank you. You are using a 32-bit machine and, currently, NCBI provides precompiled binaries for 64-bit machines only. You may be able to compile them from the source code (xtract.go and rchive.go, each of which needs to be built together with common.go, and with some third-party libraries on hand). ...
written 14 days ago by vkkodali1.1k
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Comment: C: Which is the best way to work with NCBI data obtaining online partial informatio
... Technically this can be done using Entrez Direct tools by fetching the entire flatfile in XML format using the `efetch` tool and parsing it using the `xtract` tool. But I'd expect the code to be a bit more readable with biopython. What have you tried so far? ...
written 15 days ago by vkkodali1.1k
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Comment: C: Entrez Direct problems
... @ioanahrom could you please send me the output of `uname -sm` from your VM? ...
written 15 days ago by vkkodali1.1k
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Comment: C: Are there any tools that can create a very basic GTF file from contig sequences
... Typically, one uses a GTF file to represent annotation. Is your contig annotated? If not, you can create a 'fake' GTF file with just one feature that goes from the first nt to the last nt of the contig. You won't need the sequence for this but the name, length of the contig. The specs for GTF file a ...
written 29 days ago by vkkodali1.1k
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Answer: A: Can Ncbi Blast Only Search A Special Region In Database For Hits?
... If you have the fasta sequence of chr1 on disk, you can use the `-subject` and `-subject_loc` options. From `blastn -help`: -subject Subject sequence(s) to search * Incompatible with: db, gilist, seqidlist, negative_gilist, db_soft_mask, db_hard_mask -subject_loc Location ...
written 29 days ago by vkkodali1.1k
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Comment: C: Taking information from a .txt and converting it to fasta
... Why not just parse the `ACCESSION` lines, get the accession and download the sequences in FASTA format using Entrez Direct? Do you expect these sequences to be somehow different from the versions that are public? ...
written 8 weeks ago by vkkodali1.1k
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Answer: A: Extracting the assemblies from wgs accessions
... Batch Entrez is expecting a list of GIs. If you can get those somehow, you can use Batch Entrez. Alternately, assuming you want to download the sequences in FASTA format, you can use [Entrez Direct](bit.ly/entrez-direct) for this as follows: epost -input -db nuccore -format acc \ | efe ...
written 9 weeks ago by vkkodali1.1k
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Comment: C: NCBI Saccharomyces cerevisiae GENE_INFO has child taxon ID instead of parent.
... Looks like everything with an SGD gene identifier has the more specific taxid. Perhaps that's because SGD data is specific to S288C strain? ...
written 9 weeks ago by vkkodali1.1k

Latest awards to vkkodali

Teacher 24 days 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?
Guru 29 days ago, received more than 100 upvotes.
Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: Change NBCI accession numbers to UNIPROT identifiers
Centurion 10 weeks ago, created 100 posts.
Scholar 3 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 3 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 3 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 3 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 3 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 4 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 4 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 4 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 4 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 4 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 4 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 4 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?
Teacher 4 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 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?
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?
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 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 5 months ago, created an answer that has been accepted. For C: Strange esearch behavior
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?
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 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?

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