User: chrisclarkson100

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Posts by chrisclarkson100

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differential RNA seq analysis
... I am having trouble selecting a proper GTF file to perform differential RNA-seq analysis (in mm9), using annotation for protein coding genes (or at least all genes, but not pseudogenes). Importantly, I want at the end the quantification of gene expression per gene (not per transcript). Example comma ...
rna-seq written 20 months ago by chrisclarkson10080 • updated 20 months ago by Friederike5.2k
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can one assess the how well the output of ChromHMM fits the data given to it?
... I have implemented an analysis with ChromHMM, with many histone marks as input. I used a range of different numbers for states and assessed the output of each. for i in {1..10} do java -mx1600M -jar ~/ChromHMM/ChromHMM.jar LearnModel -p 6 ChromHMM_binary ${i}_e $i mm9 done Across a ...
chip-seq chromhmm written 2.2 years ago by chrisclarkson10080
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Answer: A: The web page at ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra
... After contacting SRA. It appears that they have done away with the 'SRX' experiment directory: *"The size of the SRA prevents the use of an FTP tree centered around experiments and had to be taken down. If you really need to use the old method of an FTP tree then look at the Runs organized by a stud ...
written 2.2 years ago by chrisclarkson10080
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Comment: C: The web page at ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra
... Thank you for this information but when I try to access the following ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX134/SRX1342333 (also not available). I then search it on the SRA database: SRX1342333 like you did and it is available.... However I just can't seem to access ...
written 2.2 years ago by chrisclarkson10080
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SRA has done away with SRX experiment directories on FTP site: The web page at ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/.... might be temporarily down
... I have been trying all day to access different SRA files on the GEO database but keep being met with '404' kind of error- stating that the site is down. I have tried on two separate computers and get the same result... taking the following path as an example: ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sr ...
software error written 2.2 years ago by chrisclarkson10080
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sam to bam header not being retained
... I have a series of sam files that I would like to convert to bam files and merge into one bam file. The downstream analysis that is to be performed on the files requires them to have header lines. example: head -n 30 input1/input1.sam @HD VN:1.0 SO:unsorted @SQ SN:chrM LN:16571 @S ...
sequence written 2.3 years ago by chrisclarkson10080 • updated 2.3 years ago by Pierre Lindenbaum125k
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PFM for CTCF in mm9 extremely difficult to find- or does one exist?
... Apologies for the naive question but I am new to the field of Position Frequency matrices (PFMs). I am trying to find a PFM for CTCF binding in the mm9 version of the mouse genome... I have searched JASPAR, TRANSFAC and http://ccg.vital-it.ch/pwmtools/pwmbrowse.html. None of the databases in these ...
assembly written 2.3 years ago by chrisclarkson10080 • updated 2.3 years ago by jared.andrews074.2k
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Comment: C: separating bed file into separate files for every 100000 base pairs
... Hi, thank you for this, In your GitHub example you input: first_fit.py hg19.gapped_extents.bed 100 1e8 I have tried your example on my own data and it looks encouraging but I am looking to write the lines within a certain base pair range to separate files. This script does not seem to do that. The ...
written 2.3 years ago by chrisclarkson10080
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separating bed file into separate files for every 100000 base pairs
... I have a really large bed file (24 GB) and I want to separate it into different files for every million base pairs. I have done it the pure programming way but this really slow #python file=open(sys.argv[1], 'r') lines=file.readlines() #print lines start=[] end=[] chr=[] ...
assembly written 2.3 years ago by chrisclarkson10080
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gc content file for human genome large and difficult to parse into separate chromosome files
... I have just downloaded the following 'gc content' documenting file: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/hg19.gc5Base.txt.gz The file contains data for all chromosomes in hg19. **it is not in bed format which makes it difficult to parse in terms of separating into chromosome files ** ...
assembly written 2.3 years ago by chrisclarkson10080 • updated 2.3 years ago by igor9.1k

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