User: svp

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svp90
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90
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Bangalore
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snijesh
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Posts by svp

<prev • 19 results • page 1 of 2 • next >
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Why 'filterByExpr' does not eliminate low read counts from the expression data?
... I estimated DEGs from RNASeq using edgeR method. But the final DEG list has several genes with low counts and are having high Fold change logFC logCPM F PValue FDR Ctrl1 Ctrl2 Str1 Str2 Gene1 7.673 -2.658 33.203 1.27E-05 0.000118 0 0 0.738954 0.657007 Ge ...
filterbyexpr degs edger rna-seq written 18 days ago by svp90 • updated 16 days ago by Gordon Smyth1.6k
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Answer: A: How do I run a .fastq single-end file in rsem-calculate-expression?
... Remove `--paired-end` from your command and run as follows: rsem-calculate-expression --num-threads 8 --time --star $fastq $(file_directory_output) ...
written 9 weeks ago by svp90
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Answer: A: How to get reference genome sequence given species name
... If you are using conda conda install -c bioconda ncbi-genome-download or simply python pip install ncbi-genome-download You can use following command in a bash script to download the genome list=["Actinomyces_viscosus", "Corynebacterium_matruchotii"] for i in list; do ncbi- ...
written 3 months ago by svp90
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Answer: A: depth calculation for targeted resequencing
... As an update you can use ###To get the mean depth of coverage bedtools coverage -a $bedfile-b $bamfile -mean > mean.bedgraph ###output the per base read depth for each region in the BED file using bedtools bedtools coverage -a $bedfile -b $bamfile -d > per.base.depth.bedgraph ###cal ...
written 3 months ago by svp90
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What is the difference of output samtools depth and samtools view -c on location of bam file?
... hi I have used following command to calculate depth of target regions in my bed file samtools depth -ab target_interval.bed 12345XX.bam > sample_depth.txt And I used following command to see how many reads are mapping to particular region samtools view -c 12345XX.bam chr1:111212724-111 ...
count bam samtools depth written 3 months ago by svp90 • updated 12 weeks ago by jkbonfield370
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Comment: C: Compute mean depth coverage for exome data with paired end, overlapping, feature
... My bam file samtools view -H test.bam | grep @HD @HD VN:1.6 SO:coordinate @SQ SN:chr1 LN:248956422 @SQ SN:chr2 LN:242193529 @SQ SN:chr3 LN:198295559 @SQ SN:chr4 LN:190214555 @SQ SN:chr5 LN:181538259 @SQ S ...
written 3 months ago by svp90
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Comment: C: Compute mean depth coverage for exome data with paired end, overlapping, feature
... lscpu Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian CPU(s): 40 On-line CPU(s) list: 0-39 Thread(s) per core: 2 Core(s) per socket: 10 Socket(s): 2 NUMA node(s): 1 Vendor I ...
written 3 months ago by svp90
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Comment: C: Compute mean depth coverage for exome data with paired end, overlapping, feature
... Hi, I used the command `bedtools coverage -a BED -b [BAM] -mean > MeanCoverageBED.bedgraph` to generate mean depth of coverage cat taregts.bed #CHR START END Gene chr1 11106936 11107192 MTOR chr1 11107388 11107655 MTOR chr1 11108018 11108369 MTOR chr1 11109097 11109459 M ...
written 3 months ago by svp90
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Comment: C: Tools To Calculate Average Coverage For A Bam File?
... what is content of `genome.txt` ...
written 3 months ago by svp90
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How to extract coverage of custom target regions (bed file) from a bam file?
... I have a bed file and a bam file. I need to find the coverage of target intervals listed in bed file by mapping over bam file? head target.bed #CHR START END Gene chr1 11106936 11107192 MTOR chr1 11107388 11107655 MTOR chr1 11108018 11108369 MTOR chr1 11109097 11109459 MTOR ...
bedtools coverage written 3 months ago by svp90

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