User: Linda

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Linda160
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160
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Last seen:
6 years, 10 months ago
Joined:
7 years, 8 months ago
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Posts by Linda

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Differential Expression Using Trinity Transcripts
... Michael, thanks for taking the time to solve this. The script is from the Analysis directory in http://sourceforge.net/projects/trinityrnaseq/ Apologies for taking long to respond. ...
written 6.8 years ago by Linda160
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Comment: C: Differential Expression Using Trinity Transcripts
... I tried a putting missing NA values to 0.00 and that produced another error. Please check the edited question. Thanks for your help. ...
written 6.8 years ago by Linda160
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Comment: C: Differential Expression Using Trinity Transcripts
... I am not sure about that. I suppose the length of the transcripts comes into play since looking at the code it seems to use the Trinity.fasta file to calculate the transcript length only. ...
written 6.8 years ago by Linda160
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Differential Expression Using Trinity Transcripts
... I am trying to perform Differential expression using transcripts from Trinity and the edgeR package. I am essentially using the steps on http://trinityrnaseq.sourceforge.net/analysis/diff_expression_analysis.html this page. Everything goes fine until I try edgeR itself. 23:22 linda SO_564$ ~/softw ...
trinity differential rna edger written 6.9 years ago by Linda160 • updated 6.8 years ago by Michael Dondrup45k
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Strange Behavior Filtering Reads With Samtools
... I am trying to filter the results of a paired end alignment with samtools. I would like to get all reads where both the pairs are unaligned. I tried samtools view -f 12 R28.bam | cut -f1-9|head HWUSI-EAS570R_0028:2:96:4625:6148#0 141 Contig18298 1907 0 100M = 1907 0 HWUSI- ...
filter bam samtools written 7.1 years ago by Linda160 • updated 7.1 years ago by Istvan Albert ♦♦ 78k
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Answer: A: Convert A Text File Into A Fasta File
... Yes. With some added text to identify the sequence. ...
written 7.1 years ago by Linda160
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Filter Reads Where Both A Read And Its Pair Is Unmapped.
... I have a bam file with all reads. I would like to filter out reads where both the read and its mate are unaligned. If either of them is aligned, I would like to keep both. Would samtools view -F 12 file.bam work? Thanks, ...
next-gen samtools mapping sequencing written 7.1 years ago by Linda160 • updated 7.1 years ago by Leszek4.0k
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Annotating Rna-Seq Data Using A Reference Genome.
... I have RNA-seq reads from a non-model organism. I used cufflinks to identify transcripts. Is there an existing pipeline to BLAST these transcripts to a model organism's proteins to identify orthologs? ...
rna blast written 7.3 years ago by Linda160 • updated 5.8 years ago by Zhidkov560
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Comment: C: How To Obtain Encode Tfbs Using The Ucsc Genome Browser
... At this point I am looking at all the encode tfs. ...
written 7.4 years ago by Linda160
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How To Obtain Encode Tfbs Using The Ucsc Genome Browser
... I am interested in finding all known Transcription Factor Binding sites for a list of genes from the ENCODE dataset. How could one automate that? From the tables it appears that each TF has its own table. Thus, I could obtain promoters for my set of genes and find its intersection with the table of ...
binding encode transcription written 7.7 years ago by Linda160 • updated 2.1 years ago by Biostar ♦♦ 20

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