User: bioinforesearchquestions

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Posts by bioinforesearchquestions

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Comment: C: Comparing the WG sequenced isolate against the other same genus isolates on the
... I annotated both the contigs.fasta using PROKKA. Then I used the isolateA.gbk and isolateB.gbk for generating the mauve output. Then I tried reordering the contigs using the isolateA.gbk and isolateB.gbk. Brigs output online coin flip simulator ...
written 3 months ago by bioinforesearchquestions270
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Comment: C: Comparing the WG sequenced isolate against the other same genus isolates on the
... Hi genomax, As discussed, the isolateA (denovo assembly carried out) assembled contigs.fasta has been used as the reference and created the required index files. Then the FASTQ files of isolateB has been aligned against the isolateA contigs.fasta (reference) using BWA. Then using callvariants.sh I ...
written 3 months ago by bioinforesearchquestions270
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Comment: C: Comparing the WG sequenced isolate against the other same genus isolates on the
... This is the error There was a problem with the search. Please, contact Help Desk and include RID P07DS4TZ01R Informational Message: [blastsrv4.REAL]: Error: Process size limit exceeded, resulting in SIGXFSZ (25). ...
written 3 months ago by bioinforesearchquestions270
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Comment: C: Comparing the WG sequenced isolate against the other same genus isolates on the
... Genomax, I tried blasting contigs > 500bp (42 contigs) against the "nr database" and optimize for "Highly similar sequences (megablast)" option selected. I got an error. Similarly I used only one contig (the largest contig) against the nr database and optimize for "Highly similar sequences (meg ...
written 3 months ago by bioinforesearchquestions270
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Comment: C: Comparing the WG sequenced isolate against the other same genus isolates on the
... Yeah, I checked that on the commandline. That's why I asked it says I need sam and bam input. My requirement is not to compare isolate A and isolate B with a reference sequence. I need to compare isolate A with isolate B and then identify SNPs. I have two contigs fasta file. For instance, then I ne ...
written 3 months ago by bioinforesearchquestions270
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Comment: C: Comparing the WG sequenced isolate against the other same genus isolates on the
... For callvariants.sh, can I use the input file in FASTA format? I am not going to do the below step for generating a sam file, because I have isolate A contig.fa and isolate B contig.fa. `bbmap.sh in=0001.fastq in2=0002.fastq out=bbmap_mapped.sam ref=H37Rv_reference.fa` callvariants.sh in=isola ...
written 3 months ago by bioinforesearchquestions270
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Comment: C: Comparing the WG sequenced isolate against the other same genus isolates on the
... Hi genomax, I have been told to do just comparison using BLAST by using the whole genome bacterial isolate against the sequences in the NCBI. First going to do BLAST as the person. I think the BLAST output is going to give multiple matching entries with different sequenced genome. What can they inf ...
written 3 months ago by bioinforesearchquestions270
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Comment: C: Heatmap with custom gene labels annotated on the rows
... Thanks, Viz. As you mentioned I gave the specific gene names on the rowNames variable and assigned it to labRow. It is printing only those genes. But the gene names are overlapped. I am trying to fix it and it would be great to have gene name protrude with an arrow. ...
written 3 months ago by bioinforesearchquestions270
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Comment: C: Heatmap with custom gene labels annotated on the rows
... I am checking out the complex heatmap links. Looks interesting. Thanks for sharing the useful link. ...
written 3 months ago by bioinforesearchquestions270
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Comment: C: Comparing the WG sequenced isolate against the other same genus isolates on the
... Apologies for missing that information, I was exactly not sure how many sequences I am going to consider for the comparison. Thanks for your suggestions. ...
written 3 months ago by bioinforesearchquestions270

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Popular Question 11 months ago, created a question with more than 1,000 views. For Is there a way to annotate existing VCF file with known disease-causing mutations?
Popular Question 11 months ago, created a question with more than 1,000 views. For Is there a way to annotate existing VCF file with known disease-causing mutations?
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