User: bitpir

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bitpir130
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Posts by bitpir

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help with interpreting metagenomic metatranscriptomic data
... Hi, I'm not quite certain how to interpret the data below and would like to seek your opinion on it. I have meta-genomic and meta-transcriptomics of a sample, and calculated the relative abundance/activity of each taxa. The rel. activity/abundance are calculated as proportion of reads mapped to eac ...
meta-transcriptomic meta-genomic written 5 months ago by bitpir130
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Comment: C: relationship between relative abundance and relative activity
... I think that is something I am struggling with too. I think what I want to get at is to figure out which organism is transcribing the most, i.e most viable? ...
written 6 months ago by bitpir130
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relationship between relative abundance and relative activity
... Hello, I have a bunch of meta-transcriptomics data and I would like to identify which organism is the most active. I plan to calculate TPM/RPKM for each organism and the figure out the "most-active" organism that way. However, I find that this method is over-simplified as I am not taking into accoun ...
meta-transcriptomics rna-seq written 6 months ago by bitpir130 • updated 4 months ago by Biostar ♦♦ 20
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measure relative abundance from rna-seq
... What a good way to calculate relative abundance using metatranscriptomics of environmental (e.g. soil) samples, without having to do metagenomic sequencing? ...
meta-transcriptomics rna-seq written 7 months ago by bitpir130
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how to speed up cdhit clustering?
... I'm trying to run CDHIT to cluster ~250M of cds at nucleotide/protein levels. These are mostly NR-like sequences from NCBI. According to the paper it takes ~ 140 mins to cluster 4M seqs with 8 core. When I run the job, it took > 12 hours to process 1M seqs. I've tried increasing the #cpu to 24 bu ...
protein clustering nucleotide clustering cdhit written 7 months ago by bitpir130
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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 9 months ago by bitpir130
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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 9 months ago by bitpir130 • updated 9 months ago by h.mon26k
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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 9 months ago by bitpir130 • updated 9 months ago by RamRS22k
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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 10 months ago by bitpir130
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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 11 months ago by bitpir130

Latest awards to bitpir

Appreciated 4 months ago, created a post with more than 5 votes. For A: how to plot multi pheatmap into one figure
Popular Question 6 months ago, created a question with more than 1,000 views. For fold enrichment calculation for exome sequencing
Popular Question 10 months ago, created a question with more than 1,000 views. For fold enrichment calculation for exome sequencing
Popular Question 12 months ago, created a question with more than 1,000 views. For fold enrichment calculation for exome sequencing
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: how to plot multi pheatmap into one figure
Scholar 22 months ago, created an answer that has been accepted. For A: do blast search using gi numbers
Popular Question 2.4 years ago, created a question with more than 1,000 views. For samtools counting unique mapped reads

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