creating refseq table with coding and non-coding genes

[Ceiler, Jessika]

Hi,

 

I´m trying to create a refseq table for all 37 mitochondrial genes (human). The problem is,  I can create one table for the 13 coding genes, and one for the other ones. But I can´t figure out how to merge the tables, as the table header of both tables differ.

 

Following data were put into the table browser:

Clade: Mammal

Genome: human

Assembly: Dec. 2013 (GRCh38/hg38)

Group: Genes and Gene Predictions

Track: NCBI RefSeq

Table: RefSeq All (ncbi RefSeq)

Region: position chrM: 1-16569

Output format: all fields from selected table

 

(by using this version, I get a table with the 13 coding genes, by changing the field “table” to RefSeq Other (ncbiRefSeqOther), I receive the other genes in another table).

 

I would need the following output with all 37 genes (actually I only get this for the coding genes):

#bin

name

chrom

strand

txStart

txEnd

cdsStart

cdsEnd

exonCount

exonStarts

exonEnds

score

name2

cdsStartStat

cdsEndStat

exonFrames

 

 

I already tried to solve it by creating an intersection, but it also didn´t work for me.

 

 

Thanks a lot for your help

 

[Brian Lee]

Dear Jessika,

Thank you for using the UCSC Genome Browser and your question about merging the data from the ncbiRefSeq and ncbiRefSeqOther tables and providing the information you were sharing to help understand the steps you have been taking.

There may be a solution where you can combine these by converting them to an intermediate BED format (http://genome.ucsc.edu/FAQ/FAQformat.html#format1) that we use to display custom track data.

The ncbiRefSeqOther track is stored in a different schema as you described: http://genome.ucsc.edu/cgi-bin/hgTables?db=hg38&hgta_group=genes&hgta_track=refSeqComposite&hgta_table=ncbiRefSeqOther&hgta_doSchema=describe+table+schema

Compared to the ncbiRefSeq track which is stored in our general genePred format for gene prediction tracks: http://genome.ucsc.edu/cgi-bin/hgTables?db=hg38&hgta_group=genes&hgta_track=refSeqComposite&hgta_table=ncbiRefSeq&hgta_doSchema=describe+table+schema

When in the Table Browser you could set the output to "BED" and this will transform both of these tracks into data like this:

ncbiRefSeq:

chrM 3306 4262 YP_003024026.1 0 + 3306 4262 0 1 956, 0,

ncbiRefSeqOther:

chrM 576 647 rna164617 0 + 647 647 0 1 71, 0,

Once you have these individual files downloaded in BED from these two tables for chrM you can combine them with a UNIX sort command like the following: sort -k1,1 -k2n,2n coding.bed noncoding.bed > all.bed

Here is an example where that resulting all.bed has then be uploaded to visualize as a third custom track (which you can also just extract from this session if you go to the Table Browser): http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=brianlee&hgS_otherUserSessionName=hg38_chrM

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further public questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee
UC Santa Cruz Genomics Institute

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