User: rioualen

gravatar for rioualen
rioualen260
Reputation:
260
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Trusted
Location:
France
Last seen:
6 days, 9 hours ago
Joined:
2 years, 9 months ago
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Posts by rioualen

<prev • 55 results • page 1 of 6 • next >
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Bedtools window: getting feature from bedfile instead of GFF3 file
... Hello, I want to get features from a GFF3 file by using a bedfile and betools window. From what I understand from the documentation (![screencap][1] attached), I should get the desired result (features from B), however it seems that I get feature from the bedfile instead (file A). I'm using this ...
bedtools window written 4 months ago by rioualen260 • updated 4 months ago by Alex Reynolds23k
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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 7 months ago by rioualen260
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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 months ago by rioualen260
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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 months ago by rioualen260
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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 months ago by rioualen260
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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 months ago by rioualen260 • updated 7 months ago by h.mon14k
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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 8 months ago by rioualen260
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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 10 months ago by rioualen260
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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 11 months ago by rioualen260
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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 11 months ago by rioualen260

Latest awards to rioualen

Popular Question 6 weeks ago, created a question with more than 1,000 views. For Looking for ways to download ChIP-seq datasets programmatically in a pipeline
Appreciated 4 months ago, created a post with more than 5 votes. For C: Get chromosome sizes from fasta file
Great Question 4 months ago, created a question with more than 5,000 views. For Get chromosome sizes from fasta file
Popular Question 4 months ago, created a question with more than 1,000 views. For Looking for ways to download ChIP-seq datasets programmatically in a pipeline
Popular Question 4 months ago, created a question with more than 1,000 views. For Get chromosome sizes from fasta file
Student 4 months ago, asked a question with at least 3 up-votes. For Get chromosome sizes from fasta file
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Get chromosome sizes from fasta file
Scholar 8 months ago, created an answer that has been accepted. For A: Get chromosome name from RefSeq format for C.elegans
Student 13 months ago, asked a question with at least 3 up-votes. For Differences between trimming tools: cutadapt, bbduk and sickle
Popular Question 23 months ago, created a question with more than 1,000 views. For Get chromosome sizes from fasta file
Scholar 2.4 years ago, created an answer that has been accepted. For A: Get chromosome name from RefSeq format for C.elegans
Scholar 2.8 years ago, created an answer that has been accepted. For A: Get chromosome name from RefSeq format for C.elegans

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