User: tiago211287

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tiago2112871.1k
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Posts by tiago211287

<prev • 206 results • page 1 of 21 • next >
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Comment: C: Bioinformatics question regarding multilevel pie chart
... Maybe Adobe Illustrator? ...
written 4 days ago by tiago2112871.1k
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Comment: C: Deconvolve bulk expression data into individual immune components.
... Maybe Helpful? https://www.nature.com/articles/s41467-018-08023-x ...
written 4 days ago by tiago2112871.1k
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Comment: C: ATAC-seq DE analysis
... Your link does not work anymore. Could you update it? Thanks! ...
written 3 months ago by tiago2112871.1k
0
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Comment: C: bam file merge
... In http://www.htslib.org/doc/samtools-1.2.html, it says, > -h is specified the @SQ headers of input files will be merged into > the specified header, otherwise they will be merged into a composite > header created from the input headers. If in the process of merging > @SQ lines for coor ...
written 7 months ago by tiago2112871.1k
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Comment: C: Filtering rRNA from RNAseq data
... You can normally align the reads against genome + annotation (gencode), using STAR for example which can count the number of reads/feature. Then just check the annotated rRNA gene count percentage. You would need "good" samples as a control of what is normal/bad. ...
written 8 months ago by tiago2112871.1k
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Comment: C: want to pick up the strongest peaks in all the duplicates
... Have you already called your peaks? You can Use MACS2 for peak calling. To only then, choose strong peak signals. I would also use deeptools to access Chip-Seq Sequencing quality and statistics. ...
written 8 months ago by tiago2112871.1k
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Comment: C: How to use GNU parallel to download SRA files
... Actually, there is, using max-procs 1, you avoid loops. ...
written 12 months ago by tiago2112871.1k
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Comment: C: Using Bowtie-2 for global (genome) sequence alignment
... Are you doing synteny analysis? ...
written 12 months ago by tiago2112871.1k
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Comment: C: How long does it take to map a data of 800 MB using STAR ?
... What is your RNA-seq material, and What is the reference genome are you using ? ...
written 12 months ago by tiago2112871.1k
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Comment: C: i meet an error when i run the cuffmerge
... Tip: When posting code, use the code sample button to make it easier to read. "EOF marker is absent" means that your BAM file has been truncated. Did Tophat produce a BAM or a SAM file? How did you convert from sam to bam? ...
written 12 months ago by tiago2112871.1k

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Commentator 14 hours ago, created a comment with at least 3 up-votes. For C: Gviz: How to plot transcripts with grouping given transcript names and a TxDb?
Popular Question 12 weeks ago, created a question with more than 1,000 views. For rMATS error in the instalation test
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Great Question 4 months ago, created a question with more than 5,000 views. For What exactly means the Dispersion Plot DESeq2?
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Guru 8 months ago, received more than 100 upvotes.
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Appreciated 8 months ago, created a post with more than 5 votes. For C: about editing SAM/BAM files
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