User: windsur

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windsur0
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Posts by windsur

<prev • 8 results • page 1 of 1 • next >
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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 6 weeks ago by windsur0 • updated 6 weeks ago by Pierre Lindenbaum106k
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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 weeks 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 8 weeks 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 8 weeks 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 8 weeks ago by windsur0
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[mem_sam_pe] paired reads have different names. Without -p
... Hello, I am newbi in processing fasq files, but it is the first time that happened to me. I downloaded the L00N_RN_00N.fastq.gz, and joined in two fastq files (i.e. _R1.fastq.gz and _R2.fastq.gz). Then I load the genome reference to memory and I make a loop samples for BWA, but today I have an error ...
alignment next-gen bwa written 8 weeks ago by windsur0
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Answer: A: Annotate .bed file with gene names
... Is it possible do the same thing from a bam file? I generated the bed file using bamtobed but I do not know what option should I choice to get the name of the gene and the exon. thanks! ...
written 9 months ago by windsur0
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List of Exons per gene bad covered
... Dear all, this is my first post. I 'm new on NGS and I have some questions that I hope you can guide me. I want to create a python script to calculate the coverage. But I would like an output with headers as: sampleID, gene, chr, exon, start, end, and avg cov. For that I tried with bedtools b ...
python exon coverage written 9 months ago by windsur0

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