User: zhao03

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zhao0330
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Posts by zhao03

<prev • 41 results • page 1 of 5 • next >
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why the different peaks by HINT-ATAC all under the zero line and motif Activity Score are negativate
... Hi, i used HINT-ATAC to find motif of S3 and S5 sample, and then, i used rgt-hint differential to discover the different motif between S3 and S5, however, the result figure shows all the motif Activity Score are negativate. how can i understand? thank you ![enter image description here][1] [1]: ...
chip-seq written 7 weeks ago by zhao0330
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"Idents" can not be use in seurat
... Hi, three kind of clusters i discoverd by different dim, now i want to use result of res.0.4 to plot UMAP. However, there is error when i used the command as fllowing: Idents(D3_APLNR)<-"res.0.4" Error in UseMethod(generic = "Idents<-", object = object) : no applicable method for 'Id ...
software error rna-seq written 8 weeks ago by zhao0330 • updated 8 weeks ago by jomo018610
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Got the negative value when used ComBat to Adjust batch effects
... Hi, i used combat to remove the batch bais, however, there are some negative numbers in the result matrix. what is the means of those negative number, can i use this matrix to find the different gene? i inputted FPKM for running combat. the command is combat_edata1 = ComBat(dat=edata, batch ...
software error R written 9 weeks ago by zhao0330 • updated 9 weeks ago by geek_y11k
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Answer: A: removing batch effects using ComBat and SVA
... Hi, i also used combat to remove the batch bais, however, there are some negative numbers in the result matrix. what is the means of those negative number, can i use this matrix to find the different gene? i inputted FPKM for running combat. ...
written 9 weeks ago by zhao0330
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are there some tools or software can find the different peak of ATAC-seq
... Hi i got the ATAC-seq peaks by MACS2 cellpeak, How can i find the different peak between case and cotrol? thank you! ...
genome chip-seq written 11 weeks ago by zhao0330 • updated 10 weeks ago by Rory Stark790
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what is the result files of MACS2 bdgdiff
... hi, i used to find the difference peak of ATAC-seq by MACS2 bdgdiff, but i cant undersand what the means of the fourth column in results, the command is macs2 bdgdiff --t1 S5_treat_pileup.bdg \ --c1 S5_control_lambda.bdg \ --t2 S3_NT_treat_pileup.bdg \ ...
chip-seq atca-seq written 11 weeks ago by zhao0330
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what is the mean of "%" in DAVID Gene-annotation enrichment analysis
... Hi, when i ran gene enrichment in DAVID , i got the result like this, however , i don't understand the column of "%". Term Count % PValue List Total Pop Hits Pop Total GO:0070062~extracellular exosome 1179 39.93902439 2.15E-295 2911 2811 18224 thank you for your help!~ ...
gene software error written 5 months ago by zhao0330 • updated 5 months ago by Jean-Karim Heriche23k
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mutect2 can not identify the indel that can be found in bam file
... i used mutect2 calling a pair of sample of WES. i can see the indel in bam file ,but the result of mutect2 did not have it. form the bam of mutect2 result, i can see the total read of this indel is 282, the number read of DEL is 52, INS is 32. the command is nohup java -jar /home/D/ref/gatk/ga ...
genome snp sequencing written 5 months ago by zhao0330 • updated 5 months ago by ATpoint38k
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Answer: A: where can i download small_exac_common_3_hg19.vcf and idx file for GATK GetPileu
... i have got it. picard can transport the b37 to hg19. java -Xmx6g -jar /home/D/ref/picard/picard.jar LiftoverVcf \ I=small_exac_common_3_b37.vcf \ O=small_exac_common_3_hg19.vcf CHAIN=b37tohg19.chain REJECT=rejected_variants.vcf R=/home/D/ref/hg19/ucsc.hg19.fasta ...
written 5 months ago by zhao0330
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where can i download small_exac_common_3_hg19.vcf and idx file for GATK GetPileupSummaries
... Hi, where can i download small_exac_common_3_hg19.vcf and idx file for GATK GetPileupSummaries ? the web only support hg38,ftp://ftp.broadinstitute.org/bundle/ thank you! ...
genome software error snp written 5 months ago by zhao0330

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Popular Question 11 weeks ago, created a question with more than 1,000 views. For i can't find the SRR sample on NCBI FTP, such as SRR018260

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