User: singh.vijender

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Posts by singh.vijender

<prev • 8 results • page 1 of 1 • next >
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Answer: A: bwa mem low depth and fluctuating plot
... The plot looks fine to me. What read depth are you expecting? From the graph, it appears to have a read depth of 100+, I think that is pretty decent. On the question of peaks, there will always be regions in the genome which will over amplify in PCR amplification (hence sequenced multiple times) s ...
written 10 months ago by singh.vijender30
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Answer: A: hisat2 warning message dunring alignment of fasta file with reference genome
... The quickest test I would do is to check the insert size distribution of 1st million reads and if the size is zero then both files R1 and R2 have same data otherwise if the insert size distribution matches what is expected from library prep, I would consider it a bug in hisat2 and proceed further in ...
written 10 months ago by singh.vijender30
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Batch effect in RNAseq
... ![PCA plot of triplicates][1] Figure A ![enter image description here][2] Figure B The distribution of replicates from an RNA-seq study is plotted on the PCA plot as shown in the figures (plotted using top 500 highly variant genes). (1) Figure A: Looking at the distribution what is your opinion ...
rna-seq written 10 months ago by singh.vijender30 • updated 10 months ago by Devon Ryan91k
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Answer: A: ExAC includes WES of phenotyped population
... From my ***limited understanding***, ExAC was created to have a reasonable comparison data set (Reference) for childhood-onset Mendelian diseases. It will make sense not to include individuals with severe pediatric diseases. SNP allele frequency will be biased to those SNPs which are associated with ...
written 19 months ago by singh.vijender30
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Comment: C: Fetch pairs of discordantly aligned reads
... Thanks again, Will try it and leave a note on how did it go. ...
written 20 months ago by singh.vijender30
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Comment: C: Fetch pairs of discordantly aligned reads
... Thanks Pierre, Can I specify reference/chromosome of my first read, such that I can fetch one read aligned to a specific chromosome of the discordant pair and the other anywhere else? ...
written 20 months ago by singh.vijender30
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Fetch pairs of discordantly aligned reads
... I am trying to get discordant aligned reads from a bam file especially reads that are aligned to two different chromosomes/references. I tried samtools view to fetch reads aligned to one chromosome but this does not pull/include the second read which might have aligned to different chromosome. I a ...
genome alignment written 20 months ago by singh.vijender30 • updated 20 months ago by d-cameron2.1k
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Answer: A: Miranalyser For Mirna Prediction
... I have not used miRAnalyser but if you want to make bowtie index for transcriptome sequences (fasta format), use `bowtie-build` function of bowtie (http://bowtie-bio.sourceforge.net/manual.shtml#the-bowtie-build-indexer). same is true if using bowtie2 instead of bowtie. General usage is `bowtie-buil ...
written 23 months ago by singh.vijender30

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