User: tiago211287

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tiago2112871.0k
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Posts by tiago211287

<prev • 203 results • page 1 of 21 • next >
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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 11 weeks ago by tiago2112871.0k
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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 3 months ago by tiago2112871.0k
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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 3 months ago by tiago2112871.0k
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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 7 months ago by tiago2112871.0k
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Comment: C: Using Bowtie-2 for global (genome) sequence alignment
... Are you doing synteny analysis? ...
written 7 months ago by tiago2112871.0k
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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 7 months ago by tiago2112871.0k
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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 7 months ago by tiago2112871.0k
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Answer: A: How to remove duplicate sequences in fasta file using python?
... This task can be accomplished with [FASTA/Q Collapser][1] quickly. [1]: http://hannonlab.cshl.edu/fastx_toolkit/commandline.html ...
written 7 months ago by tiago2112871.0k
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Comment: C: Too many differentially expressed genes in RNA-seq?
... Here is a little tip for your volcano plot: Make a column with information about who is DEG, and who is not DESeq.Result$super <- DESeq.Result$log2FoldChange > 1 & DESeq.Result$padj < 0.01 DESeq.Result$sub <- DESeq.Result$log2FoldChange < -1 & DESeq.Result$padj & ...
written 8 months ago by tiago2112871.0k
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Comment: C: How to use GNU parallel to download SRA files
... You are totally right. I made it myself when I was learning. A way of using without upsetting coworkers is limit the network band with less or equal to 50 Mbps "-l50m" and always set the --maxprocs parameter in parallel to a low value. Talk with the admin is a good idea. ...
written 8 months ago by tiago2112871.0k

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Popular Question 9 days ago, created a question with more than 1,000 views. For rMATS error in the instalation test
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