User: tiago211287

gravatar for tiago211287
tiago211287890
Reputation:
890
Status:
Trusted
Location:
Brazil
Last seen:
3 days, 22 hours ago
Joined:
3 years, 5 months ago
Email:
t**********@gmail.com

Posts by tiago211287

<prev • 200 results • page 1 of 20 • next >
0
votes
2
answers
197
views
2
answers
Comment: C: How to use GNU parallel to download SRA files
... Actually, there is, using max-procs 1, you avoid loops. ...
written 3 days ago by tiago211287890
1
vote
1
answer
170
views
1
answers
Comment: C: Using Bowtie-2 for global (genome) sequence alignment
... Are you doing synteny analysis? ...
written 23 days ago by tiago211287890
0
votes
0
answers
180
views
0
answers
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 24 days ago by tiago211287890
1
vote
2
answers
204
views
2
answers
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 24 days ago by tiago211287890
1
vote
4
answers
266
views
4
answers
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 26 days ago by tiago211287890
0
votes
3
answers
257
views
3
answers
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 27 days ago by tiago211287890
0
votes
2
answers
197
views
2
answers
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 28 days ago by tiago211287890
1
vote
2
answers
197
views
2
answers
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 28 days ago by tiago211287890 • updated 28 days ago by GenoMax42k
0
votes
3
answers
194
views
3
answers
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 28 days ago by tiago211287890
1
vote
3
answers
257
views
3
answers
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 28 days ago by tiago211287890

Latest awards to tiago211287

Popular Question 23 days ago, created a question with more than 1,000 views. For How can I Get png figures of UCSC genome browser automatically?
Scholar 4 weeks ago, created an answer that has been accepted. For A: Mapping My gene list within chromosome bands
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?
Popular Question 5 months ago, created a question with more than 1,000 views. For Question about the DESeq2: log2foldchange contradictory
Popular Question 5 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 5 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 5 months ago, created an answer with at least 3 up-votes. For A: Must know algorithms before attending a bioinformatics interview
Popular Question 6 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 6 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 6 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 7 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 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 11 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 11 months ago, created an answer that has been accepted. For A: Mapping My gene list within chromosome bands
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)
Commentator 15 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 15 months ago, created an answer with at least 3 up-votes. For A: Must know algorithms before attending a bioinformatics interview
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Must know algorithms before attending a bioinformatics interview
Popular Question 16 months ago, created a question with more than 1,000 views. For DESeq input preparation
Popular Question 17 months ago, created a question with more than 1,000 views. For DESeq input preparation
Appreciated 21 months ago, created a post with more than 5 votes. For Can Tophat2 Align a Book?
Appreciated 21 months ago, created a post with more than 5 votes. For C: about editing SAM/BAM files
Teacher 21 months ago, created an answer with at least 3 up-votes. For C: about editing SAM/BAM files
Popular Question 23 months ago, created a question with more than 1,000 views. For What exactly means the Dispersion Plot DESeq2?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1001 users visited in the last hour