User: Morello Salesman

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Posts by Morello Salesman

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Comment: C: How to run SPANDX3.2
... ./SPANDx.sh -r k96243 -m yes -a yes -o haploid BP23.fastq.gz BP3504.fastq.gz BP6260.fastq.gz BP6887.fastq.gz BPZUSM.fastq.gz Reference = k96243 SNP matrix will be generated? yes VCF files will be annotated with SnpEff? yes Organism = haploid The following parameters will be used ---------------- ...
written 16 days ago by Morello Salesman0
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Comment: C: How to run SPANDX3.2
... If I directly run SPANDx.sh, it says "SPANDx.sh: command not found" ...
written 16 days ago by Morello Salesman0
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Comment: C: How to run SPANDX3.2
... I followed the SPANDX_Manual_V3.2.pdf and my command line looks like this. perl SPANDx.sh -r k96243 -o haploid -m yes -i yes -a yes -p PE B83_R1.fastq.gz B83_R2.fastq.gz ...
written 16 days ago by Morello Salesman0 • updated 16 days ago by zx87549.6k
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How to run SPANDX3.2
... Is there anyone who can help me with running Spandx 3.2? I downloaded the file from https://sourceforge.net/projects/spandx/, and every time I try to run the program it shows this: Organism = haploid Output directory and directory containing sequence files = /home/user/spandx/SPANDx_v3.2 /S ...
snp written 17 days ago by Morello Salesman0 • updated 17 days ago by Pierre Lindenbaum130k
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Comment: C: How to contiguate miseq assembly for Burkholderia
... I QCd my reads then I used Trim galore for quality and adapter trimming. ...
written 5 weeks ago by Morello Salesman0
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Comment: C: How to contiguate miseq assembly for Burkholderia
... I got 500 nodes after removing short contigs <500 bp. ...
written 6 weeks ago by Morello Salesman0
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Comment: C: How to contiguate miseq assembly for Burkholderia
... I want to have chromosomes in each file (I do not want to join the chromosomes together). ...
written 6 weeks ago by Morello Salesman0
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Comment: C: How to contiguate miseq assembly for Burkholderia
... I'm interested in comparative genomics (Against clinical reference genomes for essential and virulent genes). The BPk96243 genome that I'm interested in has both of its chromosomes (BX571965, BX571966) uploaded as separate entities. So I want to make something like that (I know this won't be complet ...
written 6 weeks ago by Morello Salesman0
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Comment: C: How to contiguate miseq assembly for Burkholderia
... Any recommendations for that? Also for further analysis, should I use two files (like chr1, chr2)? ...
written 6 weeks ago by Morello Salesman0
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How to contiguate miseq assembly for Burkholderia
... I have a Burkholderia pseudomallei sequence (Miseq paired-end) and I want to perform comparative genomics against reference genomes (BPk96243, MSHR1435 and others). I already did the spades assembly but it had many nodes (700+). I can use abacas to order/align it against a reference genome but Burkh ...
assembly alignment written 6 weeks ago by Morello Salesman0 • updated 6 weeks ago by andres.firrincieli860

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