User: MAPK

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MAPK1.4k
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Posts by MAPK

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Comment: C: How can I analyze this data in Deseq?
... @Kevin Blighe Thanks Kevin for your answer. Yes, I wanted to look for miRNA-like reads with differential expression between samples. I have seen some papers using DESeq for these reads and wanted to give it a try. ...
written 2 days ago by MAPK1.4k
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Comment: C: How can I analyze this data in Deseq?
... This is smallRNA seq data. ...
written 2 days ago by MAPK1.4k
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How can I analyze this data in Deseq?
... I have my data called `count.mat`. count.mat <- structure(list(Sample_1 = c(2968, 1701, 272, 249, 186, 1598, 98, 9, 563, 1003, 278, 242, 137, 625, 614, 494, 681, 475, 3, 89), Sample_2 = c(2057, 1237, 339, 688, 289, 1354, 265, 17, 402, 793, 343, 267, 389, 477, 838, 663, 741 ...
rnaseq R deseq2 deseq written 2 days ago by MAPK1.4k
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Comment: C: Extract coverage from each nucleotide position of a genome in a bam file
... Thanks, does this also separate based on strand? Is there a way to sort the output according to bed file's chromosome order. My alignments in bam file are in different chromosomal order (eg. Ch16, Ch15, Ch14...Ch1). ...
written 12 days ago by MAPK1.4k
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Comment: C: Extract coverage from each nucleotide position of a genome in a bam file
... Thanks, but couldn't make this work on individual base positions. ...
written 12 days ago by MAPK1.4k
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Extract coverage from each nucleotide position of a genome in a bam file
... Hi All, I have a bed file called `my_region.bed` as below: Ch1 0 3951982 my_region 0 + Ch2 0 3683506 my_region 0 + Ch3 0 3351453 my_region 0 + Ch4 0 2873318 my_region 0 + Ch5 0 2822964 my_region 0 + Ch6 0 2483831 my ...
bed bam coverage written 12 days ago by MAPK1.4k
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coverage plot for all chromosomes
... I have RNASeq data and wanted to plot coverage on both positive and negative strands of the species I am studying. I wanted to plot it like this (https://davetang.org/muse/2013/09/07/creating-a-coverage-plot-in-r/), but I was only able to plot for 1 chromosome. My organism has 16 chromosomes and I w ...
rna-seq written 16 days ago by MAPK1.4k
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Cross assembly of metagenomics
... I am working on metatranscriptomic data and wanted to use this tool available here: https://edwards.sdsu.edu/crass/# I have assembled my transcriptomic data using Trinity and have got Trinity.fasta file. However, this tool also requires ace format file, which I don't have. What do I need to do to ge ...
rna-seq written 24 days ago by MAPK1.4k
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Comment: C: Help with the perl script to extract mismatches
... I normally work in R, but this problem is complicated to work in R. ...
written 8 weeks ago by MAPK1.4k
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Comment: C: How can I map certain values for gene locus against genome?
... Thank you so much, I just got it :) ...
written 4 months ago by MAPK1.4k

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