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
... 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 1 hour ago by bioinforesearchquestions250
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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 hours ago by bioinforesearchquestions250
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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 21 hours ago by bioinforesearchquestions250
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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 22 hours ago by bioinforesearchquestions250
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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 1 day ago by bioinforesearchquestions250
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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 2 days ago by bioinforesearchquestions250
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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 2 days ago by bioinforesearchquestions250
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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 2 days ago by bioinforesearchquestions250
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Heatmap with custom gene labels annotated on the rows
... Hi friends, I would like to generate a heatmap something similar to the below image with custom genes. I am using heatmap.2 function in R. What parameters should I play with to get the labels as in the image. ...
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Comment: C: Comparing the WG sequenced isolate against the other same genus isolates on the
... Yes, I checked it, as per their website currently it is unsuitable for datasets with more than 50 bacterial genomes. But I suspect the task 1 might have more than 50 bacterial genomes. For the task2, I need to compare isolate A and isolate B and identify variants. Do you mean I need to consider one ...
written 3 days ago by bioinforesearchquestions250

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Great Question 8 weeks ago, created a question with more than 5,000 views. For How to find On-Target and Off-Targer percentage of reads?
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Popular Question 5 months ago, created a question with more than 1,000 views. For Trying to filter vcf file using SNPSIFT tool. It throws an error message
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Popular Question 8 months ago, created a question with more than 1,000 views. For Filtering multisample VCF based on genotype using SnpSift filter
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Popular Question 10 months ago, created a question with more than 1,000 views. For Filtering multisample VCF based on genotype using SnpSift filter
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