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Questions related to Bioinformatics
Dear all, I made a simple linear regression model with the same scale (i.e. X variables, and Y variable). I need to run this for each year. How to determine incremental significance of added IV's...
19 May 2020 5,128 4 View
I'm trying to find a bioinformatics/database resource besides something like malariatools, which has gene/protein function predictions based on genome loci context information, however databases...
15 May 2020 5,974 0 View
I'm trying to generate a fasta file from a reference including variants in a vcf file. I'm using bcftools and it works. My problem is that I would like to create a fasta where only the mutated...
14 May 2020 5,149 3 View
Whenever I try to add a reference fasta file for computing the GC content in the GetBamCounts function: my.countsV6
12 May 2020 5,276 5 View
I have generate indexes using bowtie2, the generated indexes are with *.bt2 not *.bt2l, so this gives error while generating indexes using tophat2. Can anyone help me to get rid of this error?
04 May 2020 9,920 0 View
The results show me the presence of plasmids, and compares them with plasmids from the database, but I can't find their locations, thank you!
17 April 2020 5,599 1 View
I want to download a specific gene from multiple genomes. In this case, I want to download just the S gene from different coronaviruses. I would like to be able to provide taxonomic IDs and the...
15 April 2020 4,586 5 View
I have differentially expressed circular RNA candidates. Are there any data, database or bioinformatical pipeline to extract circular RNAs can potentially be translated into proteins? Thank you!
11 April 2020 8,621 1 View
Grettings everyone. I'm analyzing transcriptomic data of a mollusc searching new Antimicrobial Peptides and i want to determine if they have putative transcription factor binding sites. Anyone...
23 March 2020 9,249 3 View
Hello everyone, These days I've read many papers regarding RNA-seq and its corresponding analysis, I found when it comes to assembly part, almost every paper would tell how many contigs and...
22 March 2020 3,125 2 View
Hi everyone; I need data on comparison of apolipoproteins expression in the normal liver. I want to know which type of the apolipoproteins is highly expressed than others in the normal...
16 March 2020 877 3 View
I'm identifying plant sequences (for rbcL gene) obtained from insect gut contents using BLAST in the NCBI GenBank database. Most of the sequences have 95-96% of matched identity and a few have of...
01 March 2020 8,251 4 View
I am finding it pretty difficult doing an online program. Does anyone know of any school offering a short program or continuing education in Bioinformatics?
28 February 2020 6,249 3 View
Suppose we have the following single nucleotide polymorphic variant: Reference DNA sequence S0 = G T G A C T G A G C C T Variant DNA sequences S1 = A T G A C T G A G C C T S2 = G A G A C T G A G...
02 February 2020 8,917 4 View
What common study types exist in NGS research and wide genome profiling related to risk assessment studies ? What are the appropriate publishing standards of reporting results from the above...
02 February 2020 6,981 4 View
Hello everybody, I am new with the meta-analysis in Genome Wide Data so I have this doubt. I have read METAL documentation, which is by far the most used meta-analysis software in both EWAS and...
02 February 2020 2,158 2 View
The current Legionella pneumophila SBT databse ( http://bioinformatics.phe.org.uk/legionella/legionella_sbt/php/sbt_homepage.php / http://www.ewgli.org/ ) maintaint by Public Health England’s...
02 February 2020 7,961 3 View
Hello, I wish to sequence the genomes of approx. 70 Clostridium perfringens strains for bioinformatic analyses. I was hesitating between 2 Illumina technologies: MiSeq and Hiseq. Could you help...
02 February 2020 8,841 3 View
When I get results from sequencing, they often overlap only partly or not at all. In such case it's easier to align them with the "parental" sequence (of what I expect), to see where they align....
02 February 2020 8,527 3 View
Hi everybody What is the relationship between the population's genetic and geographic distance? I appreciate your help. Best regards
02 February 2020 4,941 9 View
I have target sequences that I want to blast and then extract from all Glires reference genomes on NCBI along with 500bps upstream and downstream of each top match for a few hundred sequences....
02 February 2020 770 3 View
Hi, Any help will be much beneficial. Thanks Rocktim
02 February 2020 7,483 3 View
I have a list of reference SNPs IDs (rsid) and I need to retrieve the associated diseases ... what are the suitable bioinformatics tools or databases?
02 February 2020 4,978 1 View
Dear All, I did qPCR. How can I calculate CT values for this qPCR data? How can I quantify cDNA? What about down-regulation and up-regulation of genes? Please find the attached excel file and...
22 January 2020 5,692 0 View