User: vkkodali

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vkkodali2.1k
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Posts by vkkodali

<prev • 253 results • page 1 of 26 • next >
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Comment: C: Elink to get PMID associated with a BioProject or SRA entry
... If an identifier from BioProject, BioSample, SRA, GEO, etc are mentioned in the publication, they get picked up automatically and the inter-database connections are made. That said, an author or user can (and highly encouraged to) write to NCBI Helpdesk to notify that a publication is no now out and ...
written 2 days ago by vkkodali2.1k
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Comment: C: Elink to get PMID associated with a BioProject or SRA entry
... This specific BioProject does not seem to be linked to any PubMed article. Do you know if the author has published a paper? ...
written 2 days ago by vkkodali2.1k
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Answer: A: How to download all Pseudomonas aeruginosa Genomes from NCBI Genomes database?
... You can download these data directly from NCBI using the Datasets tool. Check out: [NCBI Datasets][1] for more details. [1]: https://www.ncbi.nlm.nih.gov/datasets ...
written 7 days ago by vkkodali2.1k • updated 7 days ago by genomax91k
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Comment: C: Batch Entrez outputs nothing
... I am able to load them just fine. I am able to click on the "Retrieve records for 10 UID(s)" link and go to Nucleotide with the 10 records. ...
written 5 weeks ago by vkkodali2.1k
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Comment: C: How to retrieve sets of protein sequences?
... Yup, that will do it. I never used fish myself but I have seen issues like these come up when I tried to use bash loops in cshell. Glad to hear that it's working for you now. ...
written 5 weeks ago by vkkodali2.1k
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Comment: C: How to retrieve sets of protein sequences?
... What do you mean it does not do anything? Please try it without the `-s` parameter for `curl`. I just tried it and I see 3 FASTA sequences in the `uniprot_seqs.fasta` file. ...
written 5 weeks ago by vkkodali2.1k
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Comment: C: BAM to FASTQ discards most reads as singletons though flagstat says otherwise
... Yup, I get the correct set of data now. Thank you! ...
written 11 weeks ago by vkkodali2.1k
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Answer: C: BAM to FASTQ discards most reads as singletons though flagstat says otherwise
... They are position-sorted which is the `samtools sort` default. I did not see any mention of the bam file being queryname-sorted. Sorting the bam file using `samtools sort -n in.bam -o out.querysort.bam` and then using `samtools fastq` returns the expected result. ...
written 11 weeks ago by vkkodali2.1k
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BAM to FASTQ discards most reads as singletons though flagstat says otherwise
... I have a bam file that returns the following when I run `samtools flagstat`: 37353420 + 61518 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 0 + 0 supplementary 9068558 + 0 duplicates 29533570 + 48760 mapped (79.07% : 79.26%) 37353420 + 61518 paired in sequenc ...
bam samtools written 11 weeks ago by vkkodali2.1k
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Answer: A: Unkown NCBI genome chromosomes
... For definitions of these terms, see: https://www.ncbi.nlm.nih.gov/grc/help/definitions/ - chr11_KI270721v1_random -- unlocalized scaffold - chrUn_GL000195v1 -- unplaced scaffold - chr19_KV575247v1_alt -- alternate locus or a novel-patch sequence - chr22_KQ759762v1_fix -- fix-patch sequence ...
written 11 weeks ago by vkkodali2.1k

Latest awards to vkkodali

Teacher 5 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?
Supporter 10 weeks ago, voted at least 25 times.
Scholar 11 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?
Teacher 11 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?
Scholar 11 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?
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 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 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 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 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?
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?
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?
Appreciated 8 months ago, created a post with more than 5 votes. For A: Obtain N50 stats from NCBI for all Hymenoptera genome assemblies
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?
Scholar 10 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 10 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 10 months ago, created an answer that was upvoted at least 5 times. For A: Obtain N50 stats from NCBI for all Hymenoptera genome assemblies
Teacher 10 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?
Appreciated 10 months ago, created a post with more than 5 votes. For A: Obtain N50 stats from NCBI for all Hymenoptera genome assemblies
Scholar 10 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 11 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 11 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 11 months ago, created a post with more than 5 votes. For A: Obtain N50 stats from NCBI for all Hymenoptera genome assemblies
Teacher 11 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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