User: Luke

gravatar for Luke
Luke220
Reputation:
220
Status:
Trusted
Location:
Turin, Italy
Last seen:
1 year, 9 months ago
Joined:
6 years, 10 months ago
Email:
l**********@gmail.com

MSc in Biomolecular Science, University of Turin, Italy

PhD student at University of Milan

Bioinformatician at National Research Council - Milan, Italy

Posts by Luke

<prev • 18 results • page 1 of 2 • next >
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Answer: A: Output Of Chip-Seq Data Analysis Using Macs
... Hi Vikas, Have a look at this paper. In discussion the authors say: "[...] when tag counts from ChIP and controls are not balanced, the sample with more tags often gives more peaks even though MACS normalizes the total tag counts between the two samples. [...] we suggest to ChIP-Seq users that ...
written 4.6 years ago by Luke220
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Answer: A: How To Extract A Subset Of Reads In Fastq Using An Id List?
... I've found a quick solution with cdbfasta and cdbyank tools. First you have to index your fastq with cdbfasta, then you can search for the IDs in fastq with cdbyank. For more info http://sourceforge.net/projects/cdbfasta/ Thank you, Luke ...
written 5.2 years ago by Luke220
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6 follow
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How To Extract A Subset Of Reads In Fastq Using An Id List?
... Hello! I obtained a list of unmapped reads IDs from my BAM file and I want to remap only the unmapped reads with other parameters. How can I extract the subset of unmapped reads from my original fastq file? Thank you in advance, Luke ...
fastq bam written 5.2 years ago by Luke220 • updated 2.2 years ago by Brian Bushnell13k
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How Can I Verify If My Chip-Seq Control/Input Data Is Enough Covered By Sequencing Tags?
... Hi Dears, as written in the title, do you know any software/tool to test if my control/input data is sufficiently covered by sequencing and if the distribution of tags is similar to an uniform distribution? Thank you. Best regards, Luke ...
software chip-seq written 5.3 years ago by Luke220 • updated 11 days ago by Biostar ♦♦ 20
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Comment: C: How Can I Convert A Bed File Into A Tab File With Paired End Reads On The Same R
... Dear Sean, thank you! I'm studing python, it's a very powerful language! I tried your script, but it works fine only for the first two record of my file. In the following rows it prints the first read, then it prints the second read twice in the following row. Is it a problem of iteration? Or variab ...
written 5.6 years ago by Luke220
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How Can I Convert A Bed File Into A Tab File With Paired End Reads On The Same Row?
... Hi guys! I have a file like this one (obtained from bed file using awk): scaffold00002b 209798 209823 HWUSI-EAS1825_0024_FC:8:1:6009:1105 scaffold00002b 209802 209838 HWUSI-EAS1825_0024_FC:8:1:6009:1105 scaffold00002d 43627 43652 HWUSI-EAS1825_0024_FC:8:1:8703:1105 scaffold00008e 2 ...
bed conversion file written 5.6 years ago by Luke220 • updated 5.6 years ago by Sean Davis23k
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How Can I Obtain Genome Scaffolds Using Paired End 454 Reads And An Hybrid Assembly As Input?
... Hi. I have an hybrid assembly (454 + Illumina) of 268 contigs (genome of about 7Mb). Now I want to create scaffolds using 3k 454 paired end reads. Which tool can I use? Newbler? (I would not use MIRA). With Which options? Any suggestions? Thanks in advance ;) Luke ...
assembly scaffolding illumina written 5.6 years ago by Luke220 • updated 3.9 years ago by Richard Smith-Unna130
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Comment: C: How I Can Obtain "Product" Features From A List Of Ncbi Accession?
... I'm interested only in a brief description of the CDS product. ...
written 5.7 years ago by Luke220
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Comment: C: How I Can Obtain "Product" Features From A List Of Ncbi Accession?
... Yes, Larry, from GenBank! For example /note="CWF19-like 2, cell cycle control" under the section "gene" or /product="CWF19-like protein 2" under the section "CDS" of the GenBank file. ...
written 5.7 years ago by Luke220
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Comment: C: How I Can Obtain "Product" Features From A List Of Ncbi Accession?
... Hi Larry! I wish retrieve this information from GenBank: [...] FEATURES Location/Qualifiers [...] gene 1..3285 /gene="CWF19L2" ==> /note="CWF19-like 2, cell cycle control /dbxref="GeneID:143884" ...
written 5.7 years ago by Luke220

Latest awards to Luke

Appreciated 3.8 years ago, created a post with more than 5 votes. For How Can I Get Protein Sequence In Fasta Format Using Taxon Id?
Good Question 3.8 years ago, asked a question that was upvoted at least 5 times. For Is There Any Way To Retrieve Genes' Sequences In Fasta Format Using The Kegg Orthology Code?
Good Question 3.8 years ago, asked a question that was upvoted at least 5 times. For How Can I Get Protein Sequence In Fasta Format Using Taxon Id?
Popular Question 3.8 years ago, created a question with more than 1,000 views. For How To Extract A Subset Of Reads In Fastq Using An Id List?
Popular Question 3.8 years ago, created a question with more than 1,000 views. For How Can I Get Protein Sequence In Fasta Format Using Taxon Id?
Student 3.8 years ago, asked a question with at least 3 up-votes. For How To Extract A Subset Of Reads In Fastq Using An Id List?
Student 3.8 years ago, asked a question with at least 3 up-votes. For How Can I Get Protein Sequence In Fasta Format Using Taxon Id?
Autobiographer 3.8 years ago, has more than 80 characters in the information field of the user's profile.

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