User: David

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David160
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Posts by David

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Deseq2 with continous variable
... Hi, I would to see if there us any gene differentially expressed based on a continous variable (temperature) over age. I want to know exactly if there any genes that differ over age. I have the following design: > design(dds) = ~ Agegroup:temperature Agegroup has two factors: 20_40 and 41_70 ...
deseq2 written 3 days ago by David160 • updated 3 days ago by Kevin Blighe59k
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Comment: A: Remove fungi from human genome assemblies
... Yes i do have secondary aligments: samtools flagstat mapping.human.bam 141346 + 0 in total (QC-passed reads + QC-failed reads) 12798 + 0 secondary 44548 + 0 supplementary 0 + 0 duplicates 89377 + 0 mapped (63.23% : N/A) 0 + 0 paired in sequencing 0 + 0 read1 0 + ...
written 10 weeks ago by David160
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Comment: C: Remove fungi from human genome assemblies
... The -F 0x900 is for excluding secondary and supplementary alignments from the unmapped reads. I don´t see why secondary alignments would filter fungi unless human reads map to fungi ? ...
written 11 weeks ago by David160
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Comment: C: Remove fungi from human genome assemblies
... Yes that´s a metagenomics experiment on skin, i´m not interested in human , but bacteria and fungi. For some reasons fungi are filtered out: This is the command line: # Map ONT reads to human genome minimap2 -t10 -ax map-ont human_p38.3.fa ONT.reads.fq | samtools view --threads 10 -Sb ...
written 11 weeks ago by David160
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Comment: C: Remove fungi from human genome assemblies
... The fungi sequences are filtered together with the human genome, the reason why is because the human assemblies contain sequences that unfortunatly belong to contaminates (such as bacterial and fungi). These are hard to filter so was wondering. The following post from Brian bushnell (bbmap package ...
written 11 weeks ago by David160
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Remove fungi from human genome assemblies
... Hi, I´m mapping a set of ont long reads to the human genome: I´m using this genome version from gencode: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_33/GRCh38.p13.genome.fa.gz See description here: https://www.gencodegenes.org/human/ I´m using a skin sample so i expect to fin ...
dnaseq minimap written 11 weeks ago by David160 • updated 10 days ago by Biostar ♦♦ 20
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Answer: A: mummer dot plot
... Hi Alex, Definetly you are right (thanks for the figure)!!!!! Let me add more info to the discussion. The two genomes have been assembled from the same input pacbio dataset (RSII). The only difference is that one was assembled 3 years ago and the other yesterday with Flye. WOuld there be any expl ...
written 8 months ago by David160
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Answer: A: mummer dot plot
... Thanks Alex, these are complete genomes. A quick blast shows that the longer fragment matches plus/minus to the reference. And the small fragment also blast in plus/minus compared to the reference. However i would expect a single fragment and not two. This suggests that the small fragment is also re ...
written 8 months ago by David160
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mummer dot plot
... Hello, I have aligned two complete bacterial genomes using mummer (1 contig per genome) I´m not sure i understand well the output. Here is the mummer plot: I think the plot suggest that there are two main reverse regions. Is that correct. If so is this what is happening at the genome level. Tr ...
dotplot mummer written 8 months ago by David160
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Comment: C: What is the symmetric identity percent
... Sorry, i have updated the image ...
written 12 months ago by David160

Latest awards to David

Popular Question 6 months ago, created a question with more than 1,000 views. For Featurecounts normalize by gene length
Popular Question 6 months ago, created a question with more than 1,000 views. For Get length of the alignment from bam file
Popular Question 7 months ago, created a question with more than 1,000 views. For Get length of the alignment from bam file
Scholar 7 months ago, created an answer that has been accepted. For A: mummer dot plot
Popular Question 12 months ago, created a question with more than 1,000 views. For Download NCBI genomes using taxonomy id (taxid)
Popular Question 12 months ago, created a question with more than 1,000 views. For Design primer for a family of bacterial genes
Popular Question 12 months ago, created a question with more than 1,000 views. For How to get percent identity from bam file ?
Student 15 months ago, asked a question with at least 3 up-votes. For Download NCBI genomes using taxonomy id (taxid)
Popular Question 15 months ago, created a question with more than 1,000 views. For Normalization methods for metagenomics WGS data (not 16S data)
Popular Question 16 months ago, created a question with more than 1,000 views. For Download NCBI genomes using taxonomy id (taxid)
Popular Question 17 months ago, created a question with more than 1,000 views. For Download NCBI genomes using taxonomy id (taxid)
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