User: windsur

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windsur0
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Posts by windsur

<prev • 13 results • page 1 of 2 • next >
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Comment: C: BWA. Allocate memory
... hey Bastian, yes it was sucessfull ...
written 3 months ago by windsur0
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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 3 months ago by windsur0
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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 3 months ago by windsur0
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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 3 months ago by windsur0
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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 3 months ago by windsur0
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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 7 months ago by windsur0 • updated 7 months ago by Pierre Lindenbaum113k
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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 7 months ago by windsur0
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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 7 months ago by windsur0
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Comment: C: [mem_sam_pe] paired reads have different names. Without -p
... Thank you! I just checked: For the first one (R1): @NS500387:143:HVKMFAFXX:1:11101:14111:1058 1:N:0:TAGGCATG+NTCCTTAC @NS500387:143:HVKMFAFXX:1:11101:6775:1061 1:N:0:TAGGCATG+NTCCTTAC @NS500387:143:HVKMFAFXX:1:11101:21397:1063 1:N:0:TAGGCATG+NTCCTTAC @NS500387:143:HVKMFAFXX:1:11101: ...
written 7 months ago by windsur0
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Comment: A: [mem_sam_pe] paired reads have different names. Without -p
... Nice! I'm going to check it right now. Thanks! If it is "0", what should I do? ...
written 7 months ago by windsur0

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