User: windsur

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windsur10
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Posts by windsur

<prev • 15 results • page 1 of 2 • next >
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Comment: A: Get Flanking Amino Acid Sequence
... Thank you Chris! But unfortunately I do not have a lot of time to learn how to use pVACtools, because I will need to use another format of my vcf file... I think there is another way faster to do what I need. Because if we have to amino acid position (e.g. G580C), with a script similar of bedtools I ...
written 6 weeks ago by windsur10
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Get Flanking Amino Acid Sequence
... Dear all, I've just perform an exome-seq and I've obtained the vcf file. Now to continue with my experiment, I need to extract the flanking regions wt and mut type of my dataset because I need to synthesize that for an immunotherapy research. I mean, in my vfc file I have a column like this: A ...
R dna-seq sequence snp python written 6 weeks ago by windsur10
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Comment: C: BWA. Allocate memory
... hey Bastian, yes it was sucessfull ...
written 6 months ago by windsur10
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Comment: C: BWA. Allocate memory
... Thanks Bastian, I will try with HISAT too. And to index my reference I have followed the steps of [GATK][1] [1]: https://gatkforums.broadinstitute.org/gatk/discussion/2798/howto-prepare-a-reference-for-use-with-bwa-and-gatk ...
written 6 months ago by windsur10
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Comment: C: BWA. Allocate memory
... Exactly! after using samtools I unload the genome reference: call('bwa shm -d',shell = True) Or should I not use samtools for the analysis you mean? ...
written 6 months ago by windsur10
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Comment: C: BWA. Allocate memory
... Thanks! I will try to add more memory and also what you said. what I use is: call('bwa mem -t' + str(args.threads) + ' -R "@RG\tID:' + sample_name + '\tLB:library\tPL:illumina\tPU:library\tSM:' + sample_name + '" ' + genome_ref + ' ' + forward_paths[i] + ' ' + reverse_paths[i] + ' > ' + sam ...
written 6 months ago by windsur10
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BWA. Allocate memory
... Dear all, I have changed the work station and now I am using Centos 7 as operating system. And if I write this I found that I think I do not have such memory as run a pipeline (in python) to analyse an exome-seq > free -h total used free shared buff/c ...
next-gen alignment memory bwa sequencing written 6 months ago by windsur10
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check genes from a list. print if match
... Hello! I haven't seen any similar question, so: I have a list of genes and several vcf files. What I would like to do is to check from the list of the genes in all vcf files from a dir, and if I get a match, return me in **one** table (e.g excel) with all the info line, the first columm should ha ...
vcf python list genes written 10 months ago by windsur10 • updated 10 months ago by Pierre Lindenbaum116k
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Answer: A: [mem_sam_pe] paired reads have different names. Without -p
... Solved! It wasn't a problem of my script. The problem was when I've tried downloading the files through Basespace of Illumina, for some reason, there was a connection problem and the files was "corrupted". what I did is downloading the files and then join the fastq files (separated). ...
written 10 months ago by windsur10
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Comment: C: [mem_sam_pe] paired reads have different names. Without -p
... @PierreLindenbaum this is the message that I get: [mem_sam_pe] paired reads have different names: "NS500387:143:HVKMFAFXX:1:11101:21856:1052", "NS500387:143:HVKMFAFXX:2:11101:12190:1028" ...
written 10 months ago by windsur10

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