User: Yingzi Zhang

gravatar for Yingzi Zhang
Yingzi Zhang40
Reputation:
40
Status:
New User
Location:
Beijing
Last seen:
3 days ago
Joined:
5 months ago
Email:
z******@yeah.net

Posts by Yingzi Zhang

<prev • 45 results • page 1 of 5 • next >
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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 days ago by Yingzi Zhang40
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Comment: C: how to set R parameter in MergeBamAlignment in Picard
... Got it. Thanks a lot. ...
written 20 days ago by Yingzi Zhang40
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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 20 days ago by Yingzi Zhang40
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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 24 days ago by Yingzi Zhang40
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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 24 days ago by Yingzi Zhang40 • updated 24 days 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 27 days ago by Yingzi Zhang40
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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 27 days ago by Yingzi Zhang40 • updated 27 days ago by zx87545.6k
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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 11 weeks ago by Yingzi Zhang40 • updated 11 weeks ago by Pierre Lindenbaum114k
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Comment: C: how to use regular expression to grasp information before "GO:" or "#N/A"
... Thank you for the suggestion. I couldn't find a answer button. I could only see "ADD REPLY" so I clicked it. sorry, are you able to modify this? Yingzi ...
written 3 months ago by Yingzi Zhang40
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Comment: C: how to use regular expression to grasp information before "GO:" or "#N/A"
... Thank you so much. :) ...
written 3 months ago by Yingzi Zhang40

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