Moderator: swbarnes2

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Posts by swbarnes2

<prev • 244 results • page 1 of 25 • next >
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Comment: C: Extract dna sequence of multiple genes from multiple bam files
... samtools fasta will not generate a reference fasta. It turns each read from a one line sam format into two line fasta format. samtools.pl should have pileup2fq, that is closer to what you want. ...
written 5 weeks ago by swbarnes22.8k
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Answer: A: align spike in database
... Make a new reference file which includes the spike-in sequences. Reindex that genome with Bowtie, realign. ...
written 8 weeks ago by swbarnes22.8k
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Comment: C: Substituting Snps On Reference Genome Assemblies
... My version of samtools 1.4 doesn't have vcfutils.pl. It does have samtools.pl, which has pileup2fq, so you might want to try that. You can make your own pileup2fa pretty easily, by editing the samtools.pl script. perl scripts are plain texts, so you can look at them easily. Find the the code b ...
written 9 weeks ago by swbarnes22.8k
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Answer: A: FastQ format (\n)
... If you are asking if it's okay to just concatenate fastq files together, yes, you can do that. You can also just 'cat' fastq.gz files together. It all works fine. No need to strip an EOF character off prior to concatenating. ...
written 10 weeks ago by swbarnes22.8k
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Answer: A: Confirming Viruses detected from NGS data
... Quick and dirty approach is to align just to virus, but you might get human reads that would better align to human genome falsely aligning to your viral genome, because that' all you gave it to match to. Better is to align to viral and human genome together. The alignment will be more accurate lik ...
written 10 weeks ago by swbarnes22.8k
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Answer: A: Extract mutations for a specific gene from a vcf file
... If you know the coordinates of the gene, you could use awk or bedtools to get all mutations in a specific genomic interval. ...
written 5 months ago by swbarnes22.8k
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Comment: C: samtools flagstat returning 0% align reads
... Go to the fasta that you downloaded for use with PASH, change all the spaces in the reference names to underscores. Remake the genome index, realign. ...
written 5 months ago by swbarnes22.8k
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Answer: A: samtools flagstat returning 0% align reads
... I wonder if having spaces in your references sequence names is the problem; Maybe Bowtie is okay with them, but PASH is not. I'd fix that, and realign. ...
written 5 months ago by swbarnes22.8k
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Comment: C: Meta-analysis of RNA-seq Data
... If you have no biological replicates, your dataset doesn't actually tell you very much. ...
written 6 months ago by swbarnes22.8k
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Answer: A: Memory usage of picard Samsort
... Simple not-very-clever solution...use grep or something to split out the files by chromosome, sort those individually, then cat them back together (with the orignal headers) ...
written 6 months ago by swbarnes22.8k

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Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
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Scholar 5 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Blast: Homology Or Similarity?
Scholar 9 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
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Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
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Scholar 3.1 years ago, created an answer that has been accepted. For A: Problem with FPKM values
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