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5

It's an A. The number refers to the position just before the |. This is clearer on different zoom levels, but I double checked by going to the very beginning of a chromosome: As you can see in the image above, the | is always after the base it refers to. I also confirmed by checking a few random positions using another genome browser which places the ...


3

You could make your own such file with FIMO, the JASPAR MEME files available via the MEME download site, and your genome build of interest (per-chromosome FASTA files from UCSC goldenpath, say), e.g., for assembly hg19 and UCSC chromosome naming scheme: $ for chr in `seq 1 22` X Y; do echo ${chr}; wget -qO- http://hgdownload.cse.ucsc.edu/goldenpath/hg19/...


3

You can link them with the kgXref table, since kgXref.refseq == refGene.name and kgXref.kgID == knownCanonical.transcript. Since it seems that knownCanonical.transcript is what you want anyway, you don't even need to join on it: mysql --user=genomep --password=password --host=genome-mysql.cse.ucsc.edu \ -A -D hg38 -e 'select concat(t.name, ".", i.version) ...


3

I stumbled across this issue after getting the same warning message from liftOver. By using the -out option of lgHgGene, the database parameter is ignored but must still be provided. The table parameter should be the second column from your GTF file. Note that you must also specify the -gtf option (otherwise it expects GFF format). In my case, the GTF file ...


2

You need to setup ssh keys. All the commands in the script are going to use ssh to run the commands. Note the tips here of how to setup ssh keys: http://genomewiki.ucsc.edu/index.php/Parasol_job_control_system#SSH_keysssh key setup


2

Check your webserver functions from the top down. You can do this from any WEB browser, even one that is on the webserver system itself. For example, does this link function: http://webserver-id/ and provide you with a home page for that WEB service ? If not, then there is not apache WEB server on that system, or is mis-configured. Next, depending upon ...


2

The current ensembl entry doesn't have a 29 either. The archived ensembl assembly lacks 29 30, and 31 and 33 and LGE64. The chromosomes after 30 are tiny, so they might not be visible in a karyotype. They probably realized that "chr 29" was really attached to some other chromosome.


2

Typical tools to use for this would be the DEXseq packages (as done here) or rMATS, which will calculate intron retention rates. I would generally suggest not summing intronic counts by gene and using that in DESeq2 (I assume that's what you meant by DESeq, since there's no reason to use the original DESeq for anything). What you'd be getting if you did ...


2

You never want to include the hgsid parameter in your url because that is the link to your current browsing session and all its specific contents. So if you send that link to someone else and then they start browsing around that link may not work correctly again in the future if you or the person you sent the link to modify your browsing session. As to how ...


2

If you need a 3-column BED, you can just use standard Unix tools: curl ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_27/gencode.v27.annotation.gtf.gz \ | gzip -dc \ | grep -wFf list.txt \ | awk -vFS="\t" '$3=="exon"{print $1"\t"($4-1)"\t"$5"\t"$9}' > out-3.bed If you need a 12-column BED: # install k8 and paftools.js curl -L http://bit....


2

You could grab exons via Gencode v27 (hg38) GFF annotations and convert them to BED via BEDOPS convert2bed/gff2bed: $ wget -qO- ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_27/gencode.v27.annotation.gff3.gz \ | gunzip --stdout - \ | awk '$3 == "exon"' \ | convert2bed -i gff - \ > exons.bed Then use grep to filter exons ...


2

Gencode is correct (when in doubt, always assume Gencode/Ensembl is correct when it differs from UCSC). What presumably happened is that the UCSC annotation pipeline noticed that Hba-a1 and Hba-a2 are nearly identical (they produce the same protein and have minimal nucleotide difference) and just misannotated.


2

Headers should not contain tabs: track type=narrowPeak name="Somite narrowPeak" description="Somite narrowPeak" Ensure that you have NO tabs on that line.


2

You could do a few command-line operations to answer this question. This assumes the use of hg38 assembly. First, get a list of genes from GENCODE: $ wget -qO- ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_28/gencode.v28.annotation.gff3.gz \ | gunzip --stdout - \ | awk '$3 == "gene"' - \ | convert2bed -i gff - \ &...


2

I think you might have changed the separator (or at least have some kind of inconsistency from the required format) for your file. Note that peak output files from MACS2 are variants of BED files. It seems you need to have a tab separator for this type of file. I copied your example file and then ran awk -v OFS="\t" '$1=$1' your_peaks.narrowPeaks > ...


2

No, there's no simple way to do that without someone writing a program tailored toward it that handles the footer section and recreates the zoom levels that follow the compressed blocks of intervals. If you wanted to write such a program, modifying bigWigCat from Kent's tools would be a reasonable tack.


1

The UCSC Data Integrator can combine multiple tracks (CpG Islands, TFBS, cCREs, etc.) into one output annotation file, and it works with any assembly you choose. You can select which output fields you want, then download the tab-delimited file. From there, you can use R, Python, and/or GNU tools such as awk and sed to coerce the data into a format which is ...


1

I don't think you need to go to R or Python to do that. In bash set -euxo pipefail for f in *.bed do bn="$(basename ${f})" on="${bn%%.bed}_with_header.bed" echo 'track type=narrowPeak name="narrowPeak"' > "${on}" cat "${f}" >> "${on}" done EDIT: I just read you want to set the name ...


1

I figured out the issue by myself. It turned out that UCSC liftover doesn't like the character ":" I removed ":" and it worked


1

Short answer: respect the case of the tool name Longer story below Thanks to terdon, I printed the PATH when the conda environment was active and listed what was in the folder where conda installed the UCSC tool. ls /mnt/home2/miska/cr517/anaconda3/envs/ucsc-netchainsubset377/bin c_rehash libpng-config mysql_config openssl pngfix libpng16-...


1

It turned out that using table browser on UCSC we could download an output with all fields. That output actually contains a GenePred file but has one extra column on the left end. The genePred file format definition is here.


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