User: rioualen

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rioualen210
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France
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1 week ago
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Posts by rioualen

<prev • 54 results • page 1 of 6 • next >
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GC content biases in RNA-seq data of A.thaliana
... Hello, I'm currently working on RNA-seq data from A.thaliana, and I have questions about quality and GC content. I guess it's normal to have a higher GC% in RNA-seq data than in the genome itself, since coding sequences usually show a bias toward GC. However, A.thaliana has a GC rate of 36% and my ...
gc athaliana mapping rna-seq written 5 weeks ago by rioualen210
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Comment: C: Extract basic info from fastq files in an efficient way?
... Oh yeah that's right, though it implies to run MultiQC in the first place. Thank you! ...
written 7 weeks ago by rioualen210
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Comment: C: Extract basic info from fastq files in an efficient way?
... Looks like what I'm looking for! Gonna dig into that :-) ...
written 7 weeks ago by rioualen210
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Comment: C: Extract basic info from fastq files in an efficient way?
... I know MultiQC is great, but I'm interested in using these numbers as variables in my pipeline :-) ...
written 7 weeks ago by rioualen210
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5 follow
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Extract basic info from fastq files in an efficient way?
... Hi, I'm looking for an easy and efficient way to get basic information from a given fastq file programmatically, like number of sequences, average sequence length, average GC%... I adapted [this code][1] but it's actually very slow for big fastq files. I was considering parsing FastQC's results bu ...
fastq fastqc written 7 weeks ago by rioualen210 • updated 7 weeks ago by h.mon9.2k
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Answer: A: "Segmentation fault (core dumped)" using sickle for trimming, depending on optio
... In case someone else is running into this issue, using shortcuts for params names avoids the problem: `-q` instead of `--qual-threshold` and `-l` instead of `--length-threshold`, specifically. So in my case the problem was not related to my VM, but to the fact that my VM was using another version ...
written 9 weeks ago by rioualen210
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Comment: C: "Segmentation fault (core dumped)" using sickle for trimming, depending on optio
... I'm sorry but I'm not the one who wrote Sickle, that's why I actually need help... ...
written 4 months ago by rioualen210
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Comment: C: "Segmentation fault (core dumped)" using sickle for trimming, depending on optio
... case 'q': single_qual_threshold = atoi(optarg); if (single_qual_threshold < 0) { fprintf(stderr, "Quality threshold must be >= 0\n"); return EXIT_FAILURE; } break; case 'l': single_leng ...
written 4 months ago by rioualen210
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Comment: C: "Segmentation fault (core dumped)" using sickle for trimming, depending on optio
... int single_qual_threshold = 20; int single_length_threshold = 20; static struct option single_long_options[] = { {"fastq-file", required_argument, 0, 'f'}, {"output-file", required_argument, 0, 'o'}, {"qual-type", required_argument, 0, 't'}, {"qual-th ...
written 4 months ago by rioualen210
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Comment: C: "Segmentation fault (core dumped)" using sickle for trimming, depending on optio
... They look normal, and again I've ran this tool on these specific files lots of times before. ...
written 4 months ago by rioualen210

Latest awards to rioualen

Scholar 9 weeks ago, created an answer that has been accepted. For A: Get chromosome name from RefSeq format for C.elegans
Student 7 months ago, asked a question with at least 3 up-votes. For Differences between trimming tools: cutadapt, bbduk and sickle
Popular Question 17 months ago, created a question with more than 1,000 views. For Get chromosome sizes from fasta file
Scholar 22 months ago, created an answer that has been accepted. For A: Get chromosome name from RefSeq format for C.elegans
Scholar 2.3 years ago, created an answer that has been accepted. For A: Get chromosome name from RefSeq format for C.elegans

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