User: max_19

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max_19150
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Posts by max_19

<prev • 48 results • page 1 of 5 • next >
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Determine level of heterozygosity
... Hi all, I am trying to determine the level of heterozygosity in my de-novo assembled genome, in order to do this I think I should measure the snp frequency. So far what I have done is called SNPs using my final assembly and then converted to VCF using below: bcftools mpileup -Ou -f ../scaffol ...
genome vcf frequency heterozygous snp written 10 months ago by max_19150 • updated 10 months ago by Brice Sarver3.5k
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Comment: C: Convert prodigal output
... This works perfectly - thank you! ...
written 11 months ago by max_19150
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Comment: C: Varying assembly statistics: Abyss & SPades
... Will try that - thank you! ...
written 12 months ago by max_19150
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Comment: C: Varying assembly statistics: Abyss & SPades
... I actually tried subsampling (Randomly select 15% of the data) and I assembled with SPades, see stats below: Assembly scaffolds # contigs (>= 0 bp) 12763 # contigs (>= 1000 bp) 1672 # contigs (>= 5000 bp) 87 # contigs ...
written 12 months ago by max_19150
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Comment: C: Varying assembly statistics: Abyss & SPades
... That is good to know, thank you! Expected assembly size is ~4.8MB. Adapters have been trimmed and I applied a quality filtering of q=30 with trimmomatic. Sequencing coverage is very high (~1000X). Once I remove those scaffolds that are very small from scaffolds.fasta, should I then remove the read ...
written 12 months ago by max_19150
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Comment: C: Varying assembly statistics: Abyss & SPades
... Thanks for your suggestion! I tried doing that and then running good_contigs.fa with QUAST, however the N50 did not change. Do you think I have to reassemble with SPades (i.e. remove all the reads which map to those contigs, then reassemble) ...
written 12 months ago by max_19150
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Comment: C: Searching and filtering uniclust databases
... Thanks for the helpful information! The uniclust download that I am using does not contain the **uniclust30_2018_08_consensus.fasta file** . I downloaded this one (uniclust30_2018_08_hhsuite.tar.gz) because I am using the database with HHsuite eventually. Here are the files that I have when I extr ...
written 14 months ago by max_19150
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Searching and filtering uniclust databases
... Hi there, Does anyone have experience with searching or filtering uniclust databases: http://gwdu111.gwdg.de/~compbiol/uniclust/2018_08/ For example if i want to search for a particular organism? or filter for only eukaryotes? (in the uniclust30db) I tried doing this with the mapping file that is ...
uniclust protein databases written 14 months ago by max_19150 • updated 14 months ago by SMK1.9k
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Comment: C: HH-suite: Segmentation fault (core dumped)
... I will try that instead! thanks for your help! ...
written 15 months ago by max_19150
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Comment: C: HH-suite: Segmentation fault (core dumped)
... I see. Each alignment is ~11,000 characters long. maybe there is a better way to go about this. I have 35 orthologous proteins (across 30 similar species) and i'd like to build an HMM profile with them and then compare them to HMM profiles in HH suite databases (profile vs profile), so I can determi ...
written 15 months ago by max_19150

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Supporter 14 months ago, voted at least 25 times.

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