User: Maria333

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Maria33310
Reputation:
10
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New User
Location:
European Union
Last seen:
3 years, 11 months ago
Joined:
5 years, 6 months ago
Email:
m****************@gmail.com

Posts by Maria333

<prev • 26 results • page 1 of 3 • next >
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Comment: C: LD Analysis between SNPs and CNVs
... Hi Benika, I am trying to do exactly the same as you and I am struggling finding a tool to do that. I have also sent the authors of the paper above an email and I am waiting for a response, but since you have faced this problem 3 months ago, can you please tell me if you found a solution to this? ...
written 3.9 years ago by Maria33310
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Comment: C: VariantsToVCF GATK toolkit
... Actually -R is usually used when a .fasta file is followed, but I tried the .bam.bai as well.. The instructions say that only the following can be used for the -V option:  This argument supports ROD files of the following types: BCF2,BEAGLE, BED, BEDTABLE, EXAMPLEBINARY, GELITEXT, RAWHAPMAP, REFSEQ ...
written 4.1 years ago by Maria33310
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VariantsToVCF GATK toolkit
... Hi, Does anyone know whether we are allowed to use bam files as the "variant file to convert" to VariantsToVCF on GATK toolkit? I'm using the following command line: java -jar ../GenomeAnalysisTK.jar -T VariantsToVCF -R example.bam.bai -o output.vcf -V example.bam  and I get: Please add an expl ...
vcf gatk bam written 4.1 years ago by Maria33310
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Comment: C: BedTools intersect - Segmentation fault
... Thank you very much for that, it helped a lot. I sorted the bed file and then used  sort -k1,1V to reverse the order so it is in ascending order.. Now I get the error: Error: The genome file sorted.bed.ascending has no valid entries. Exiting.  Do you know why is this? The files seem fine now..  Th ...
written 4.2 years ago by Maria33310
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BedTools intersect - Segmentation fault
... Hi, Has anyone experienced the "segmentation fault" error while trying to use bedtools intersect option? I am trying to see overlap exons between 2 bed files but I'm getting this error all the time. Any help will be much appreciated. Thank you ...
bedtools human exons written 4.2 years ago by Maria33310 • updated 4.2 years ago by Alex Reynolds29k
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Comment: C: download recent list of human exons
... I need them in a bed format and yes, I need the coordinates of all human exons.. I emailed 1000G but the latest version they have is from 2013 since they stopped doing sequencing..  ...
written 4.2 years ago by Maria33310
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Comment: C: download recent list of human exons
... Hi Malachi, Thanks for your response. I need to have the exact coordinates of the human exons. The latest one is located in the 1000 Genomes project website and it is from 2012.. Hope it is more clear now..   ...
written 4.2 years ago by Maria33310
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download recent list of human exons
... Hi, Does anyone know where to download the most recent list of human exons? The most recent I can find is from the 1000G and from 2012..  Thank you ...
human exons written 4.2 years ago by Maria33310 • updated 4.2 years ago by Giovanni M Dall'Olio26k
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Comment: C: Sed command for replacements
... Hi Daniel, I was using sed to transform a chromosome position and I thought it was relevant since it's under a Linux environment..  Sorry if this is irrelevant..  ...
written 4.3 years ago by Maria33310
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(Closed) Sed command for replacements
... Hi, Does anyone know how I can replace ":" with "-" in linux? I was able to remove the spaces and substitute them with ":", but now I need to remove one of the two ":" and replace it with a "-". For example: 1:12000000:13000000 into 1:12000000-13000000 I have tried it in several ways and it ju ...
sed chromosome positions written 4.3 years ago by Maria33310 • updated 4.3 years ago by Pierre Lindenbaum123k

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Popular Question 4.4 years ago, created a question with more than 1,000 views. For Samtools Depth Option For More Than One Bam Files

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