Hi, Jennifer,
I get BLAT matches, but few liftOver matches (19 out of 256 regions). Below
are the code I used.
cd /mnt/shared/GenomeLift/bayanus
#mkdir lift net psl chainRaw over bedOver
for i in {1..16} M; do faSplit -lift=lift/chr$i.lft size ../sacCer1/chr$i.fa
-oneFile 3000 /scratch/split/chr$i; done
for i in {1..16} M; do blat contig.fasta /scratch/split/chr$i.fa
raw/Sb_Sc_chr${i}.psl -tileSize=11 -minScore=100 -minIdentity=80 -fastMap;
done
cd raw; for i in {1..16} M; do liftUp -pslQ ../psl/chr$i.psl
../lift/chr$i.lft warn Sb_Sc_chr${i}.psl; done
#faToTwoBit contig.fasta Sb_contig.2bit
cd ..;
for i in {1..16} M; do axtChain -linearGap=medium -psl psl/chr${i}.psl
Sb_contig.2bit ../sacCer1/chr${i}.2bit chainRaw/Sb2Sc_chr${i}.chain; done
chainMergeSort chainRaw/*.chain | chainSplit chain stdin
cd chain; for i in *.chain; do chainNet $i ../contig.sizes
../../sacCer1/chrom.sizes ../net/${i}.net /dev/null; done
for i in *.chain; do netChainSubset ../net/$i.net $i ../over/$i; done
cat ../over/*.chain >../bedOver/over.chain
cd ..;
liftOver -minMatch=0.1 -multiple SB_Ste12_bind4.bed bedOver/over.chain
SB2SC_Ste12_bind.bed SB2SC_nomatch.txt
On Mon, May 3, 2010 at 2:31 PM, Jennifer Jackson <[email protected]> wrote:
> Hello Wei,
>
> To clarify, do you not have BLAT matches between the two species or do you
> have the matches, but it is liftOver that not mapping data? If you don't
> know, try tweaking liftOver a bit first.
>
> liftOver parameters:
> - use BED as an input (if you were using positional format)
> - use -multiple, use -minMatch 0.1
> - maybe add in a -minSizeQ 300 (or so) to keep short fragment out (that
> multiple will capture). Or leave out -minSizeQ, review, then add it back
in
> using a threshold you set based on what type of output you desire.
>
> Try the liftOver changes and let us know if this does not solve the
problem.
> If it doesn't, send back details for the processing you (your exact
> parameters based on the processes from the document) and we can provide
> feedback for loosening up the match criteria.
>
> Thanks,
> Jennifer
>
> ---------------------------------
> Jennifer Jackson
> UCSC Genome Informatics Group
> http://genome.ucsc.edu/
>
> On 5/3/10 10:52 AM, Wei Zheng wrote:
>>
>> Hello,
>>
>> I was trying to generate over.chain from S. bayanus to S. cerevisiae
>> and perform liftOver to map TFBS of S.bayanus to S. cerevisiae
>> coordinates, using the instructions on
>> http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/hg/doc/liftOver.txt.
>> However I can only get less than 10% of my TFBS lifted, the others are
>> always non-matched.
>>
>> I wonder whether you could point out some key parameters in blat,
>> axtChain, and liftOver steps for such closely related yeast species.
>> The assembly I used was sacCer1 (16 chromosomes downloaded from UCSC)
>> for S. cerevisiae and 1098 contigs (downloaded from SGD, reported in
>> Kellis 2003) for S. bayanus.
>>
>> Thank you very much!
>>
>> Wei
>> _______________________________________________
>> Genome maillist - [email protected]
>> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>
_______________________________________________
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