User: bitpir

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bitpir90
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Posts by bitpir

<prev • 45 results • page 1 of 5 • next >
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Comment: C: how to concatenate contigs from repseq?
... Absolutely! Let's say I want to combine NZ_LNUL01000001:NZ_LNUL01000133 into one whole genome sequences. These are scaffolds from a whole genome seq project on NCBI and are stored in different accessionId's. I would like to combine all these scaffolds (sometimes contigs for some other species) so th ...
written 4 weeks ago by bitpir90
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how to concatenate contigs from repseq?
... Hello, Is there a good way to concatenate the contigs from refs (from single sequencing project) to get a whole genome sequence? Is there a good bioinformatics tools out there to do this? Thanks! ...
ncbi refseq concatenate written 4 weeks ago by bitpir90 • updated 4 weeks ago by h.mon20k
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tools/resources on mixed-integer programming
... Hi there! Here's the problem I'm trying to solve: Given a pool of gene ID and their read counts -- some genes are unique to one particular species while some are shared--what is the most likely combination of species that can be present in the sample and how to calculate their relative abundance? ...
probability mixed-integer programming written 5 weeks ago by bitpir90 • updated 5 weeks ago by RamRS18k
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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 12 weeks ago by bitpir90
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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 3 months ago by bitpir90
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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 3 months ago by bitpir90 • updated 3 months ago by Devon Ryan85k
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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 4 months ago by bitpir90
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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 4 months ago by bitpir90 • updated 4 months ago by Alex Reynolds26k
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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 5 months ago by bitpir90
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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 5 months ago by bitpir90

Latest awards to bitpir

Popular Question 9 weeks ago, created a question with more than 1,000 views. For fold enrichment calculation for exome sequencing
Popular Question 4 months ago, created a question with more than 1,000 views. For fold enrichment calculation for exome sequencing
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: how to plot multi pheatmap into one figure
Scholar 14 months ago, created an answer that has been accepted. For A: do blast search using gi numbers
Popular Question 20 months ago, created a question with more than 1,000 views. For samtools counting unique mapped reads

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