User: 2012201024

gravatar for 2012201024
201220102420
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Location:
China
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4 years, 8 months ago
Joined:
4 years, 11 months ago
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2*********@njau.edu.cn

Posts by 2012201024

<prev • 12 results • page 1 of 2 • next >
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Transcriptome analysis principle
... Hill all, In my opinion, I would like to consider the transcriptome as multiple QPCR. But in the actural transcriptome analysis process, there are no ck genes, like actin et al. So I want to know how can we confirm the different treatments have a same comparison background? Many thanks in advance. ...
rna-seq written 4.7 years ago by 201220102420 • updated 4.3 years ago by Damian Kao15k
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Comment: C: Call all types of SNP and Indels
... Yeah, that is the exact I want to know. Sorry for poor English~~ ...
written 4.8 years ago by 201220102420
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Call all types of SNP and Indels
... HI, all, I have a mapping BAM file, and want to use samtools software to call the all the SNP and Indels on every site, and each variation proportion on the site, if there are several variations on one site. I notice that the samtools can only output a few SNP and Indels under default parameters. I ...
alignment sequence snp written 4.8 years ago by 201220102420 • updated 4.8 years ago by guillaume.rbt660
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(Closed) Transcriptome DGE RPKM, or FPKM
... Hi, all, I am analysising  the gene expression difference of a transcriptome DGE data. Two parameter RPKM and FPKM make me puzzled. I have known the exactly difference between these two words. But which one is better for me to do analysis. Anyon please help me. Thanks ...
rna-seq written 4.8 years ago by 201220102420 • updated 4.7 years ago by Biostar ♦♦ 20
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Convert gff format file to circos band table
... Hi, I have a genes.annotation.gff file, such as: chrC09 GazeA2 mRNA 9318184 9322857 214.6819 - . ID=BnaC09g12820D;Name=BnaC09g12820D;Alias=GSBRNA2T00000001001 chrC09 GazeA2 CDS 9322739 9322857 23.0574 - 0 Parent=BnaC09g12820D;Name=BnaC09g12820D;Alias=GSBRNA2T00000001001 chrC09 GazeA2 CDS 9322374 9 ...
ciros written 4.9 years ago by 201220102420 • updated 4.9 years ago by Alex Reynolds29k
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Comment: C: Output the color code according to number
... OK, Thank you for your advice. In fact, I'm using graphlan to draw a metagenome picture, because the software don't provid color code of heatmap, so I should get them through this method. Sorry about that. ...
written 4.9 years ago by 201220102420
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Comment: A: Output the color code according to number
... Many thanks for your reply. Furthermor, if I input a list like "1  3.5   4.5  9   2", and want to output the corresponding color code, according to a scale, how should I operate?  ...
written 4.9 years ago by 201220102420
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(Closed) Output the color code according to number
... Hi, I want to get a series of color code, like #0000FF, according to a list of number. I can set a color scale in R heatmap and draw a picture, but how to get the code list of color?  Hope somebody help. Thanks! ...
R written 4.9 years ago by 201220102420
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Comment: C: BWA/samtools output match length and SNPs number of each reads?
...   Op BAM Description M 0 alignment match (can be a sequence match or mismatch) I 1 insertion to the reference D 2 deletion from the reference N 3 skipped region from the reference S 4 soft clipping (clipped sequences present in SEQ) H 5 hard clipping (clipped sequences NOT present in SEQ) P 6 paddi ...
written 4.9 years ago by 201220102420
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Comment: C: BWA/samtools output match length and SNPs number of each reads?
... Thanks a lot. I have got MD tags through: samtools calmd [-EeubSr] [-C capQcoef] <aln.bam> <ref.fasta>. Forthermore, I want to analysis the SNPs number (even Nucleotide substitution rate) of each reads compaired with the reference. Are there some python scripts which can solve this? ...
written 4.9 years ago by 201220102420

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