User: David

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David70
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Posts by David

<prev • 68 results • page 1 of 7 • next >
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Comment: C: bedcoverage output while looking for missing genes
... Thanks Kevin, I went trough the bedtools but didn´t find clearly that it was the last 4 columns. Thanks for letting me know. ...
written 4 weeks ago by David70
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bedcoverage output while looking for missing genes
... Hi, I´m trying to identify missing genes in my bacterial assembly compared to my reference genome. I have run coverageBed as follows: coverageBed -a Staph.genomic.gff -b Staph_assembly.sorted.bam I´m not sure i understand all columns so i was wondering if you could help me on identifyong ...
bedtools written 5 weeks ago by David70 • updated 5 weeks ago by Kevin Blighe19k
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Comment: C: Get length of the alignment from bam file
... I´m more of a perl guy but can give it a try ...
written 6 weeks ago by David70
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Get length of the alignment from bam file
... Hi, I would like to know if it is it possible to get the read length of the higher alignment in a bam file having more than 85% identity. For example an output with this fields: - Read_length - Alignment_length - Percent_identity thanks ...
bam written 6 weeks ago by David70 • updated 6 weeks ago by Pierre Lindenbaum107k
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Comment: C: How to get percent identity from bam file ?
... I´ll check Nanoplot. thanks ...
written 8 weeks ago by David70
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Comment: C: How to get percent identity from bam file ?
... My bam file was generated as follows: > minimap2 -ax asm10 -t 8 canuAssembly.contigs.mmi demultiplex/BC01.fastq.gz | samtools sort -@8 -o 1.sorted.bam > > Ignoring SAM validation error: ERROR: Record 15966, Read name > 1b0bcee6-ba9e-409d-9172-4817a6e6fc4a, CIGAR covers 5190 bases but ...
written 8 weeks ago by David70
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Comment: A: How to get percent identity from bam file ?
... Here is the output ?? bioalcidaejdk -e 'stream().map(R->R.getReadUnmappedFlag()?0:(int)(100.0*(R.getReadLength()-R.getIntegerAttribute("NM"))/(double)R.getReadLength())).collect(Collectors.groupingBy(Function.identity(), Collectors.counting())).forEach((K,V)->{println(K+"\t"+V);});' ...
written 8 weeks ago by David70
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How to get percent identity from bam file ?
... I have aligned raw 1D nanopore reads to a bacterial reference assembly using BWA –MEM and got the sam and bam file. Is there a quick way to get the of percentage identity for each read from the sam/bam file ??? I would like to generate an histogram with reads count and the percent identity to the ...
bam samtools bwa written 8 weeks ago by David70
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Comment: C: Cannot align reads to plasmid
... Thanks for your response genomax. It´s an illumina 2*250bp on a single bacterial genome. It turns out that insert size average is 300, not that good, but i have quality trimmed all sequences and remove adapters and phiX genome. Here is the output from bbspplit #name %unambiguousReads u ...
written 3 months ago by David70
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Cannot align reads to plasmid
... Hi, I have sequenced a bacterial genome for which i have a reference genome (98% similarity). I have used bwa to map reads to the reference genome: bwa mem reference.fa reads.R1.fq.gz reads.R2.fq.gz I´m failing to recover the plasmid although i know it´s there. I have run the assembly using meg ...
bwa sequencing written 3 months ago by David70 • updated 3 months ago by h.mon14k

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Popular Question 5 weeks ago, created a question with more than 1,000 views. For Relative abundance fro metagenomics samples
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Student 13 months ago, asked a question with at least 3 up-votes. For Download NCBI genomes using taxonomy id (taxid)

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