User: bitpir

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bitpir80
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Posts by bitpir

<prev • 42 results • page 1 of 5 • next >
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taxa identification using signature vs alignment to refseq
... Has anyone tried and compared the taxa identified using both signatures and reference sequences? I seem to identify much more taxa from the refseq with little overlap with what i identified from signatures. In this case, which results should i trust more? ...
signatures metagenomics alignment refseq written 26 days ago by bitpir80
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finding secondary taxid using ete3 ncbiTaxa
... Hello, I'm trying to using ete3's ncbitaxa to get species-to-genus taxid's. I noticed that there are some taxid that aren't found (e.g.1913078 or 1283312). When checking ncbi website, I notice that they are secondary taxid. Is there anyway that I can still find the genus id for these secondary taxid ...
taxonomyid ete3 ncbitaxa python written 5 weeks ago by bitpir80
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difference between mapq=0 and samtools flag 0x900
... Hello, I am comparing the # of uniquely mapped reads from the same fastq (illumina paired end) to 2 reference sequences using BWA-MEM. I expect mapping to one of the reference sequences (let's call it ref A) to be have many multi-mappers and mapping the other (ref B) to be more unique. Ref A has ma ...
samtools mapq written 7 weeks ago by bitpir80 • updated 7 weeks ago by Devon Ryan82k
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Comment: C: getting a combination of all predicted genes
... Thanks for the response! I actually made a mistake in the desired result, it's corrected now. I aim to get all of the orfs predicted by mga and genemark. However, when the same orf is predicted in the same region, I'll give preference to the longer one: NC_003552.1 mga cds 1 1500 133.183 - ...
written 12 weeks ago by bitpir80
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getting a combination of all predicted genes
... Hello, I was wondering if anyone knows the best way to doing this. I have results from 2 ORF predictors, Mga and Genemark. I now want to combine all the predicted ORFs together. I would like to keep all overlapping ORFs and also the genes that are slightly longer (e.g. +10bp). The MGA result is as ...
bedtools gff written 12 weeks ago by bitpir80 • updated 12 weeks ago by Alex Reynolds25k
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Comment: C: getting feature annotations for all NCBI Refseq sequences
... Ah! Just found the [answer][1] to my question, for the second part at least :) [1]: https://www.biostars.org/p/221188/ ...
written 3 months ago by bitpir80
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Comment: C: getting feature annotations for all NCBI Refseq sequences
... great, thank you! My virus db includes [View all RefSeq and Neighbor nucleotide records][1], will all of the viruses be captured in the summary file? I was thinking of finding all the NC_ accession number to a particular assembly accession number [(e.g. NC_011750.1 --> GCF_000026345.1)][2]. I ha ...
written 3 months ago by bitpir80
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Comment: C: getting feature annotations for all NCBI Refseq sequences
... Awesome! Thank you so much for your answer, this is super helpful! Are the sequences from the Refseq/release represented in the assembly_summary_refseq.txt? And in case of viruses [e.g. https://www.ncbi.nlm.nih.gov/nuccore/LC340031.1][1], is there a similar assembly_summary file where I can get all ...
written 3 months ago by bitpir80
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getting feature annotations for all NCBI Refseq sequences
... Hi, I was wondering if there's a way to download all feature annotations (Gene; CDS; rRNA; tRNA; ncRNA; repeat_region) of all the Refseq sequences (ftp://ftp.ncbi.nih.gov/refseq/release/) from NCBI? I can't seem to find it anywhere on the web or NCBI. Something like GFF for Genbank sequences would b ...
ncbi annotation refseq cds written 3 months ago by bitpir80 • updated 3 months ago by genomax54k
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Comment: C: IGV tracks gene annotation
... I see! Got it, thank you so much for pointing out. That's really weird that Glimmer GFF has that kind of format. I'll check again with the formatting with that file. Thanks! ...
written 3 months ago by bitpir80

Latest awards to bitpir

Popular Question 10 days ago, created a question with more than 1,000 views. For fold enrichment calculation for exome sequencing
Popular Question 9 weeks ago, created a question with more than 1,000 views. For fold enrichment calculation for exome sequencing
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: how to plot multi pheatmap into one figure
Scholar 12 months ago, created an answer that has been accepted. For A: do blast search using gi numbers
Popular Question 18 months ago, created a question with more than 1,000 views. For samtools counting unique mapped reads

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