User: yiren

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yiren0
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Posts by yiren

<prev • 15 results • page 1 of 2 • next >
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Comment: C: chip seq peaks are very long
... thank you for your reply. ...
written 2 days ago by yiren0
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Comment: C: chip seq peaks are very long
... It is Transcription factor. ...
written 2 days ago by yiren0
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Comment: C: chip seq peaks are very long
... thank you for your reply. ...
written 2 days ago by yiren0
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chip seq peaks are very long
... Hello ,every one, I have a question about peaks length.I get the peaks by macs2 for chipseq data(BAMPE file),but my peaks length is very long.they almost are bigger than 500 base. this is normal right?I will list some data from my peaks file below.Help me .Thank you very much!! chr | star | end ...
chip-seq written 5 days ago by yiren0
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Answer: A: Stringtie with Gencode gtf file doesn't give any gene_ids or transcript_ids?
... Hi,biologist did you solve this question? the question is in my pipeline for RNAseq,please what can I do next ? you can view my question from this link,[https://www.biostars.org/p/411989/#412009][1] [1]: https://www.biostars.org/p/411989/#412009 Thank you very much! ...
written 5 weeks ago by yiren0
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Comment: C: Stringtie output gtf file only contains STRG,no original annotations
... thank you for you reply.input gtf file is same as annotation file .Some genes geneid are ref_gene_id,but almost genes geneid are STRG flag. ...
written 5 weeks ago by yiren0
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Stringtie output gtf file only contains STRG,no original annotations
... Hi, I am trying to generate novel genes transcripts expression following the stringtie manual. The stringtie --merge mode takes as input a list of all the assembled transcripts files (in GTF format) previously obtained for each sample, as well as a reference annotation file (-G option).The merged.g ...
rna-seq written 5 weeks ago by yiren0 • updated 5 weeks ago by MatthewP390
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Comment: C: How to do scaling in ComplexHeatmap
... thank you very much for your reply. 1.I scale my data by t(scale(t(data))). 2.I know gene1 is difference because its foldchange is bigger than 2.what I want to do is that gene2 should be shown in the same color across the samples,gene1 shoud be showm in difference color across the samples. ...
written 8 weeks ago by yiren0
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Comment: C: How to do scaling in ComplexHeatmap
... hi,I have same question.my data is below. unscaled Symbol wt_1 wt_2 wt_3 sample2_1 sample2_2 sample2_3 gene1 5.335232251 5.740785039 5.902108135 3.992369652 3.891350026 4.270974093 gene2 15.98835431 16.02484119 16.02575545 16.00483162 16.02241575 15.99473185 It is obvious that gene1 i ...
written 8 weeks ago by yiren0
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Comment: C: index genome using haploid genome.fa or diploid genome.fa?
... thank you very much h.mom. ...
written 9 weeks ago by yiren0

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