User: Carlo Yague

gravatar for Carlo Yague
Carlo Yague4.1k
Reputation:
4,100
Status:
Trusted
Location:
Belgium
Last seen:
11 minutes ago
Joined:
2 years, 11 months ago
Email:
c**********@gmail.com

Posts by Carlo Yague

<prev • 543 results • page 1 of 55 • next >
1
vote
1
answer
114
views
1
answers
Answer: A: Is there a code to find consensus motif
... In shell using grep and regular expressions: echo 'CGATCGTG TAAGCAGCTA GTCATG' | grep -o "[AT]AAGCA[ATG]..A" TAAGCAGCTA 'N' is expressed as '.', meaning that it can take any value. Multiple nucleotides at one position are put into square brackets. ...
written 13 days ago by Carlo Yague4.1k
0
votes
0
answers
106
views
0
answers
Comment: C: m6A RNA-seq using Smarter ,fastqc found many 'TTTTTTTTTTTTTTTTTTTTTTTTTTTTT' for
... Related thread: [How to remove poly T in RNA-sequencing data][1] [1]: https://www.biostars.org/p/148743/ ...
written 18 days ago by Carlo Yague4.1k
0
votes
2
answers
145
views
2
answers
Comment: C: Compute average score across multiple bed files
... Much better than my tinkering ! ...
written 25 days ago by Carlo Yague4.1k
1
vote
2
answers
145
views
2
answers
Answer: A: Compute average score across multiple bed files
... Use [bedtools merge][1] with the `-o` and `-c` option. cat a.bed b.bed c.bed | sort -k1,1 -k2,2n > merged.bed bedtools merge -c 4 -o mean -i merged.bed PS: this doesn't seem to be working as the intervals are merged (surprise !) together, regardless of the score. To make it work, I had ...
written 25 days ago by Carlo Yague4.1k
0
votes
1
answer
161
views
1
answers
Comment: C: Conversion of Fasta file
... Then you can just use [this tool][1]. There is also this [related thread.][2] Good luck ! EDIT: If you are not used to command line tools, I saw also [this one][3] with a GUI, but I didn't test it. [1]: http://qiime.org/scripts/convert_fastaqual_fastq.html [2]: https://www.biostars.org/p/16458 ...
written 4 weeks ago by Carlo Yague4.1k
2
votes
1
answer
161
views
1
answers
Answer: C: Conversion of Fasta file
... Fasta files contain only sequences, while fastq files have both sequences and quality scores. If you want to recreate a fastq file, you'll need afile with the quality scores corresponding to your sequences, such as a [QUAL file][1]. [1]: http://scikit-bio.org/docs/0.2.2/generated/skbio.io.fasta. ...
written 4 weeks ago by Carlo Yague4.1k
2
votes
3
answers
201
views
3
answers
Answer: A: RNASeq DGE : Kallisto-sleuth Vs Ballgown
... I'll just answer this one: > Can you we rely on Fold changes even if we don't have significant q-value? No, you absolutely can't. High/low log2 fold changes are highly biased toward lowly expressed genes, as you can see in the typical MA-plot below. However, the measure of the expression of tho ...
written 5 weeks ago by Carlo Yague4.1k
3
votes
0
answers
119
views
0
answers
Tool: SL-quant: finding splice-leader (SL) trans-splicing events in RNA-seq reads.
... *My first [published bioinformatics pipeline][1], that finds and quantifies scars of special splicing events (SL trans-splicing) in RNA-seq reads:* ---------- **SL-quant: A fast and flexible pipeline to quantify spliced leader trans-splicing events from RNA-seq data** The spliceosomal transfer ...
trans-splicing nematode tool rna-seq pipeline written 5 weeks ago by Carlo Yague4.1k
0
votes
0
answers
184
views
0
answers
Comment: C: Difference in BAM coverage between bedtools output and IGV coverage track
... Is your data single- or pair-ended ? Is it strand-specific ? Does it comes from RNA or DNA samples ? One notable difference between the two programs is that by default, bedtools counts increment the coverage from the left-most to the right-most read position (regardless of whether the read is spli ...
written 5 weeks ago by Carlo Yague4.1k
2
votes
0
answers
115
views
0
answers
Comment: C: samtools stats typical ranges and explicit definitions
... Mapping quality = −10 * log10 Pr{mapping position is wrong}, rounded to the nearest integer. Higher quality means higher score. For instance if samtools believed that the pobability that the mapping position is correct is of 90%, then your MQ = -10 * log10(0.1) = 10. If the probabilty is 99%, MQ=20. ...
written 5 weeks ago by Carlo Yague4.1k

Latest awards to Carlo Yague

Scholar 13 days ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Popular Question 14 days ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Popular Question 25 days ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Good Answer 11 weeks ago, created an answer that was upvoted at least 5 times. For A: The bed12 format
Scholar 3 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Popular Question 4 months ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Scholar 4 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 6 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 7 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Popular Question 7 months ago, created a question with more than 1,000 views. For Intron-aware coverage for paired-end RNA-seq data.
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 8 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Scholar 8 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Scholar 8 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 10 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Scholar 12 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Scholar 13 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1861 users visited in the last hour