User: Yingzi Zhang

gravatar for Yingzi Zhang
Yingzi Zhang50
Reputation:
50
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Trusted
Location:
Beijing
Last seen:
1 month ago
Joined:
8 months, 1 week ago
Email:
z******@yeah.net

Posts by Yingzi Zhang

<prev • 47 results • page 1 of 5 • next >
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Comment: C: Does ensembl biomart provide ortholog information incomplete?
... Apologize for my bad behavior. Thank you for your explanation. I found archive version and found it showed SIRPA ortholog relationship between human and pig. But I found gene TNF showed the same problem I described before-I can found TNF both in human and pig, but the archive version showed human do ...
written 10 weeks ago by Yingzi Zhang50
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Does ensembl biomart provide ortholog information incomplete?
... Deal all, I exported human-pig ortholog relationship information from ensembl biomart. For gene SIRPA, it showed empty information of pig gene/transcrip/protein id nor any ortholog alignment information. But for most other genes, there are such information. So I thought pig doesn't have SIRPA. How ...
ensembl written 10 weeks ago by Yingzi Zhang50 • updated 10 weeks ago by Emily_Ensembl17k
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GATK recalibrator aborted/ended without any summery report
... Dear all, I successfully built index of pig's vcf file and applied them to do GATK recalibrator. My input bam file size was about 20G, My baserecalibrator ran and didn't report any error. It only warned that "Feature file 'sus_scrofa.vcf' appears to contain no sequence dictionary. Attempting to re ...
gatk recalibrator error written 3 months ago by Yingzi Zhang50
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Comment: C: how to set R parameter in MergeBamAlignment in Picard
... Got it. Thanks a lot. ...
written 3 months ago by Yingzi Zhang50
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how to set R parameter in MergeBamAlignment in Picard
... Dear all, I am trying to use `picard MergeBamAlignment` to prepare files for GATK. I know the usage should be java -jar picard.jar MergeBamAlignment \ ALIGNED=aligned.bam \ UNMAPPED=unmapped.bam \ O=merge_alignments.bam \ R=reference_sequence.fasta Actually I wrote so. But ...
software error written 3 months ago by Yingzi Zhang50
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Comment: C: what's the difference between picard MergeBamAlignment and samtools merge
... Thank you Duo. That makes sense. Thank you for your advice also. ...
written 3 months ago by Yingzi Zhang50
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what's the difference between picard MergeBamAlignment and samtools merge
... Dear all, I want to do GATK variant calling. I have several raw-paired-end-reads fastq files for one pig individual. And I have finished mapping using bwa mem. GATK best practices (for calling germline SNPs + indels) tells that after mapping, I need to merge bam files. And it recommends `picard Me ...
software error alignment written 3 months ago by Yingzi Zhang50 • updated 3 months ago by ForeverFly20
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Comment: C: how to set metrics file when using MarkDuplicates in Picard
... Yes. I found that the Matrics is not an input file but an output file. Thank you! ...
written 4 months ago by Yingzi Zhang50
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how to set metrics file when using MarkDuplicates in Picard
... Dear all, I tried to use Picard MarkDuplicates to mark duplicates. I found `METRICS_FILE` need to be set. However, I know nothing about the "metrics"about my data. All I know is its mapping rate, etc. What should I look into and how should I set the matrics file please? Thank you. Yingzi ...
software error genome picard written 4 months ago by Yingzi Zhang50 • updated 4 months ago by zx87546.5k
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how to find the locations of protein products of a certain list of genes?
... Dear all, I need to find locations of protein products of a certain list of genes. For example, TLR1(toll like receptor 1) locates on the cell membrane. Is there any database can realize this goal? I know uniprot subcellular location. But it seems only 400+ genes are in the database. Is there any ...
software error written 5 months ago by Yingzi Zhang50 • updated 5 months ago by Pierre Lindenbaum116k

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