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Tutorial: Convert bam files to fastq in numbers as indicated in samtools flagstat stats.
samtools bam alignment fastq sequence
updated 27 days ago by 39k • written 6.0 years ago by ★ 1.5k
6
votes
2
replies
3.7k
views
Tutorial: GATK method for filtering vcf lines using GT values at all or multisample level.
genome vcf genotype variant-filtration
updated 27 days ago by 39k • written 6.0 years ago by ★ 1.5k
4
votes
0
replies
2.1k
views
Tutorial: Accurate prediction of active enhancers using PARE
ChIP-Seq histone-modification enhancer
updated 28 days ago by 39k • written 6.2 years ago by ▴ 100
3
votes
2
replies
3.5k
views
Tutorial: Galaxy Tutorial on ChIP-seq
galaxy ChIP-Seq
updated 28 days ago by 39k • written 6.2 years ago by ▴ 30
10
votes
2
replies
3.4k
views
Tutorial: Graph visualization with igraph in R
Visualization igraph Graph R Network
updated 28 days ago by 39k • written 6.2 years ago by 26k
19
votes
2
replies
3.1k
views
Tutorial: Beginner's Handbook to Next Generation Sequencing
NGS
updated 28 days ago by 39k • written 6.2 years ago by ▴ 640
2
votes
3
replies
2.4k
views
Tutorial: It's about the journey, and not the destination
R network
updated 28 days ago by 39k • written 6.2 years ago by ★ 1.2k
11
votes
2
replies
7.4k
views
Tutorial: Plotting the coverage and depth (Y-axis) statistics of a bam file along the genome (X-axis), using Samtools, awk and R.
genome plot coverage samtools
updated 28 days ago by 39k • written 6.2 years ago by ★ 1.5k
17
votes
13
replies
1.7k
views
Tutorial: Screen shots of text (please don't)!
meta
updated 28 days ago by 39k • written 6.2 years ago by 52k
59 results • Page 2 of 2
Recent Votes
Tools To Calculate Average Coverage For A Bam File?
Comment: conda: command not found: gatk.
Answer: Finding Enhancers using Genomation library
Comment: If I execute "AddOrReplaceReadGroups" on a sarted and duplicate-marked .bam fil
Answer: Extract variants/SNPs with T>G substitution from a VCF file
Comment: ChatGPT optimized for bioinformatics questions
Comment: ChatGPT optimized for bioinformatics questions
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Comment: conda: command not found: gatk. by GenoMax 130k
Follow directions provided by `GATK` project: https://gatk.broadinstitute.org/hc/en-us/articles/360035889851--How-to-Install-and-use-Conda-…
Answer: What's the correct way to store bam record in a vector and free them? by Pierre Lindenbaum 155k
You should allocate a new pointer for each SAM record. I would do something like this (not tested): ``` std::vector<bam1_t*> record_list…
Comment: Creating a local version of Clustered NR database by GenoMax 130k
Thanks for those stats. So using clustered `nr` will still require significant hardware. Though this will save time as well.
Comment: Can I send my PyMol results to a web-page as a result for a submitted query? If by Aatif Hashmi • 0
Basically I only want to show bases with disulphide bonds. like imagine I have a disulphide bond at 68 cys residue along with 145 cys. I …
Answer: How do I specify the Recalibration_data.table for "PrintReads" in GATK 4.3, if t by Pierre Lindenbaum 155k
do you want ApplyBQSR "Apply base quality score recalibration " ? https://gatk.broadinstitute.org/hc/en-us/articles/360036856671-ApplyBQSR
Comment: target vs. bait BED files for Illumina WES by Sounkou-bioinfo • 0
Hi @jacorvar , did you find the answer to that question ?
Comment: ChatGPT optimized for bioinformatics questions by Dr William Klubinski ▴ 100
That's an excellent point. A significant number of students are engaged in academic misconduct due to the use of fabricated references and …
Comment: Filtering content in heatmap to highest values by Papyrus ★ 2.5k
You mean something like this? depends on how you define "top" row or column # Create example (it is a data.table) ListerTFHeat <- …
Comment: conda: command not found: gatk. by 666billgaytes ▴ 10
Could there be an issue with your OS? I find a lot of colleagues having problems with Mac OS and much less if none at all on Windows.
Comment: ChatGPT optimized for bioinformatics questions by Dr William Klubinski ▴ 100
Great initiative :D
Answer: Extract variants/SNPs with T>G substitution from a VCF file by 4galaxy77 2.7k
Use ```bcftools view``` with the `-i` flag for including variants. ``` bcftools view -i'REF=="T" & AlT == "G"' ```
Comment: A question about the raw RNA-seq processing workflow by Dr William Klubinski ▴ 100
Hi there, the `Segmentation fault (core dumped)` seems to be related to memory issues. I would check the `core dump` that has been created …
Comment: Ensembl vep singularity by Ben_Ensembl ★ 2.2k
Hi Kiran - there is a description of downloading and running VEP with Singularity 3.5+ in the following blog post: https://www.ensembl.inf…
Comment: conda: command not found: gatk. by bestone ▴ 20
Is there anyone who can help me with this?
Comment: conda: command not found: gatk. by bestone ▴ 20
oops I didn't know I was going to evaluate them there, thanks for the warning, now I will evaluate them all. pls, could you pls with this i…
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