User: tiago211287

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tiago211287940
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Posts by tiago211287

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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 3 months ago by tiago211287940
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Comment: C: Using Bowtie-2 for global (genome) sequence alignment
... Are you doing synteny analysis? ...
written 3 months ago by tiago211287940
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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 3 months ago by tiago211287940
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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 3 months ago by tiago211287940
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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 3 months ago by tiago211287940
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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 3 months ago by tiago211287940
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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 3 months ago by tiago211287940
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Answer: A: How to use GNU parallel to download SRA files
... > As the sizes of the datasets have increased, we have found that the > traditional methods of FTP or HTTP do not have the performance > characteristics needed to support this load of data. FTP performance > degrades proportionally with the number of hops or switches the data > must t ...
written 3 months ago by tiago211287940 • updated 3 months ago by genomax47k
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Answer: C: How to count fasta sequences efficiently using (or not ) biopython
... Count the number of sequences in 1 fasta file: grep -c ">" file.fasta Count the number of sequences in several fasta files: find /home/folder/to/file/ -name "*.fasta" | parallel grep -Hc ">" {} Get the length of each instance of a fasta file: grep -v ">" 180110.fasta | awk ...
written 3 months ago by tiago211287940
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Answer: A: Too many differentially expressed genes in RNA-seq?
... It depends on your target organism and tissue. Also, adjusted p-values(padj) of 0.1 aren't big. 0.1 = 10%. In general, a good cutoff for considering a gene as a DEG is less than 0.01 (1%). Better to visualize it in the minus (-log10(padj)) scale so that anything between 0 and 1 will be a non-DEG, a ...
written 3 months ago by tiago211287940

Latest awards to tiago211287

Popular Question 21 days ago, created a question with more than 1,000 views. For Question about the DESeq2: log2foldchange contradictory
Popular Question 22 days ago, created a question with more than 1,000 views. For Question about the DESeq2: log2foldchange contradictory
Student 3 months ago, asked a question with at least 3 up-votes. For Can Tophat2 Align a Book?
Popular Question 3 months ago, created a question with more than 1,000 views. For How can I Get png figures of UCSC genome browser automatically?
Scholar 4 months ago, created an answer that has been accepted. For A: Mapping My gene list within chromosome bands
Popular Question 6 months ago, created a question with more than 1,000 views. For How can I Get png figures of UCSC genome browser automatically?
Popular Question 8 months ago, created a question with more than 1,000 views. For Question about the DESeq2: log2foldchange contradictory
Popular Question 8 months ago, created a question with more than 1,000 views. For What does this Warning in HTSeq-count means? (Warning: Mate pairing was ambiguous)
Popular Question 8 months ago, created a question with more than 1,000 views. For What is the definition of a transfrag? What is a transfrag? EDIT:(And faux-read?)
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Must know algorithms before attending a bioinformatics interview
Popular Question 9 months ago, created a question with more than 1,000 views. For What does this Warning in HTSeq-count means? (Warning: Mate pairing was ambiguous)
Popular Question 9 months ago, created a question with more than 1,000 views. For What does this Warning in HTSeq-count means? (Warning: Mate pairing was ambiguous)
Popular Question 9 months ago, created a question with more than 1,000 views. For What is the definition of a transfrag? What is a transfrag? EDIT:(And faux-read?)
Popular Question 10 months ago, created a question with more than 1,000 views. For What does this Warning in HTSeq-count means? (Warning: Mate pairing was ambiguous)
Popular Question 12 months ago, created a question with more than 1,000 views. For What does this Warning in HTSeq-count means? (Warning: Mate pairing was ambiguous)
Popular Question 13 months ago, created a question with more than 1,000 views. For What does this Warning in HTSeq-count means? (Warning: Mate pairing was ambiguous)
Popular Question 14 months ago, created a question with more than 1,000 views. For What does this Warning in HTSeq-count means? (Warning: Mate pairing was ambiguous)
Scholar 14 months ago, created an answer that has been accepted. For A: Mapping My gene list within chromosome bands
Popular Question 17 months ago, created a question with more than 1,000 views. For What does this Warning in HTSeq-count means? (Warning: Mate pairing was ambiguous)
Commentator 18 months 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?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Must know algorithms before attending a bioinformatics interview
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Must know algorithms before attending a bioinformatics interview
Popular Question 19 months ago, created a question with more than 1,000 views. For DESeq input preparation
Popular Question 20 months ago, created a question with more than 1,000 views. For DESeq input preparation
Appreciated 2.0 years ago, created a post with more than 5 votes. For Can Tophat2 Align a Book?

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