User: TrentGenomics

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Posts by TrentGenomics

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Comment: C: Very high alignment rate with bowtie2
... I do agree Macspider, but I've seen many examples where assembly quality checks by way of read representation do not exceed the range of 70-85 %. ...
written 11 days ago by TrentGenomics20
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Answer: A: Very high alignment rate with bowtie2
... These are just the tips I was looking for. I'm going to play around with the raw and trimmed reads with bowtie2 and have a look at the alignment stats. Thanks again, Kevin! I appreciate it. ...
written 11 days ago by TrentGenomics20
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Comment: C: Very high alignment rate with bowtie2
... Yes, that makes sense.I did use a >30 phred quality score when I used Trim Galore! Thanks for the explanation! ...
written 11 days ago by TrentGenomics20
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Comment: C: Very high alignment rate with bowtie2
... The reads that are mapping back at high rates are the reads that I used to generate my Trinity assembly. ...
written 11 days ago by TrentGenomics20
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Very high alignment rate with bowtie2
... Hello, My alignment rates with bowtie2 are ~95%, using paired-end reads on a de novo Trinity assembly. What I typically see in the literature is bowtie2 alignment rates of anywhere from 70-85% which is considered good. What is the reason for the rates being so high? I know that it is because mos ...
alignment rna-seq written 11 days ago by TrentGenomics20
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Predict the effect of SNPs in a VCF file generated using a Trinity assembly
... Is there software or script available to predict the effect of SNPs that have Trinity headers? Reference databases use different header formats than Trinity, so I can't use snpEff etc. There must be a solution to this. Maybe not? ...
snp written 13 days ago by TrentGenomics20 • updated 13 days ago by Istvan Albert ♦♦ 73k
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Annotate SNPs called from Trinity transcriptome assembly using annotations from Trinotate pipeline
... Hello, I have a VCF file containing SNPs called between a Trinity reference assembly and an alignment file, generated by samtools/bcftools. I have annotated the Trinity reference assembly using the Trinotate pipeline (blastx Trinity transcripts against swissprot, blastp TransDecoder predicted pr ...
assembly rna-seq blast written 26 days ago by TrentGenomics20 • updated 26 days ago by genomax33k
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Comment: C: removing part of the fasta header from multifasta file
... Correction: Must add ' to the end of 's/\path.*// to make it 's/\path.*//' Working syntax is the following: sed -e 's/\len=//' -e 's/\path.*//' MultiFasta.txt > OutLength.txt ...
written 5 weeks ago by TrentGenomics20
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Comment: C: Substituting Snps On Reference Genome Assemblies
... Would 'bcftools consensus' be a similar function to the above commands? ...
written 7 weeks ago by TrentGenomics20
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Discrepancy between number of SNP calls using samtools/bcftools when --skip-indels flag used
... Hi all, I've used the following command to call SNPs between two species: samtools mpileup -gf NFS_reference.fasta SFS_alignment_bowtie2.coordSorted.bam | bcftools call -Ou -mv | bcftools filter -s LowQual -e '%QUAL<20 || DP>100' > NFS_SFS_SNPs.var.flt.vcf The above command called ~180 ...
software error snp written 7 weeks ago by TrentGenomics20

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