User: Viz

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Viz40
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Genome Informatics Analyst

Posts by Viz

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Comment: C: Reverse Complement Reads in BAM File
... While keeping the alignment coordinates but just in reverse. ...
written 11 days ago by Viz40
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Reverse Complement Reads in BAM File
... Hello, I'm looking for a solution to reverse complement reads inside of a BAM file. I know that the obvious solution is to reverse complement reads before alignment, however that is not applicable in this case, the Fastx toolkit does not work here and seqkit provided results that weren't accurate fo ...
alignment written 11 days ago by Viz40
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Comment: C: Get unique alignment stats from SAM file with a combined genome
... Since they share the same chromosomes idxstats gives the total alignments to both, I'll check out bazam and Qualimap though and report back if they work for me, thank you. ...
written 7 weeks ago by Viz40
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Get unique alignment stats from SAM file with a combined genome
... As the title states, I have sam/bam files from alignments of our reads against an index built from two fastA genomes concatenated. From these sam files, how would I go about finding out which reads aligned to chromosome1-X in species 1 and which reads aligned to chromsome1-X in species 2. ...
genome alignment rna-seq written 7 weeks ago by Viz40
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Answer: A: (Bioinformatics) Use of Hisat2 with single end data
... If you're asking about how to align with single end data, then use the -U flag instead of flagging your first pair as -1 and second as -2. hisat2 [Flags you want] -U /path/to/reads.fq -x /path/to/genomeIndex -S out.sam If you're asking about genome indexing, it doesn't technically matter, jus ...
written 8 weeks ago by Viz40
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Comment: C: Primer3: p3in failure
... I would recommend putting your .misa file into http://bioinfo.ut.ee/primer3/ and seeing if things work from there. Also check: https://www.biostars.org/p/395170/ ...
written 8 weeks ago by Viz40
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Answer: A: How is distal enhancer defined?
... Typically a lot of papers set their own boundaries for what they want to define as a distal enhancer, especially when the distance is negligibly large, in the case of this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3654767/ they defined distal enhancers with a range of 80kb - 114kb up o ...
written 8 weeks ago by Viz40
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Answer: A: GenBank accesion number to gene id
... bioDBnet has a "DB to DB" function that allows the interchanging of any two standard gene name formats https://biodbnet-abcc.ncifcrf.gov/db/db2db.php Just enter your gene names as the Genbank input and select whatever output format you want ...
written 8 weeks ago by Viz40
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Comment: C: Heatmap with custom gene labels annotated on the rows
... Have you tried setting the parameter labRow to the value of a vector of rowNames where it contains the names? ..., labRow = rowNames, ... https://www.rdocumentation.org/packages/gplots/versions/3.0.1.1/topics/heatmap.2 ...
written 8 weeks ago by Viz40

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