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117 results • Page 3 of 3
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Tutorial: How to extract and filter SNP data from the genotyping-by-sequencing (GBS) data in vcf format using bcftools
bcftools SNP-Filtering VCF
updated 12 days ago by 38k • written 3.1 years ago by ▴ 10
2
votes
0
replies
3.8k
views
Tutorial: Calculation of TSS Scores for ATAC-seq Data
next-gen-sequencing
updated 12 days ago by 38k • written 3.7 years ago by ▴ 20
1
vote
1
reply
1.1k
views
Tutorial: Downloading GnuWin and using to convert txt to bed file for windows users
bed bed2txt sequencing txt
updated 12 days ago by 38k • written 2.6 years ago by • 0
1
vote
0
replies
161
views
Tutorial: ChIP-Seq Analysis Tutorial
Epigenetics Bowtie2 MACS2 ChIP-Seq Motif
updated 4 days ago by 70k • written 4 days ago by ▴ 20
1
vote
0
replies
1.5k
views
Tutorial: Genocad, Computer-Assisted Design For Synthetic Biology
expression
updated 27 days ago by 38k • written 9.8 years ago by 11k
1
vote
0
replies
1.9k
views
Tutorial: A short primer to pairwise alignment
pairwise-alignment blastp pam blosum
updated 2 days ago by 38k • written 7.7 years ago by ▴ 370
1
vote
0
replies
122
views
Tutorial: List of Machine Learning-Based Scoring Function Papers
machine_learning papers scoring_function docking
10 days ago by Milad ▴ 10
0
votes
0
replies
896
views
Tutorial: Apply ALoFT to identify loss-of-function somatic or germline variants
ALoFT
updated 12 days ago by 38k • written 3.8 years ago by ★ 9.3k
0
votes
1
reply
1.6k
views
Tutorial: Guide Tutorial DEAP 2.1 In Windows 7
DEAP2.1 R stata
updated 9 days ago by 38k • written 5.2 years ago by ▴ 10
0
votes
0
replies
784
views
Tutorial: VIDEO: BLAST Searches Through a Data Science Lens
Covid19 Data-Science sequence BLAST
updated 12 days ago by 38k • written 2.8 years ago by ▴ 440
0
votes
0
replies
987
views
Tutorial: Training GeneMark-EP+ ab-initio tool
abinitio training genemark annotation
updated 12 days ago by 38k • written 3.1 years ago by 7.7k
0
votes
0
replies
2.0k
views
Tutorial: Protein expression analysis
protein-analysis
updated 6 days ago by 38k • written 8.0 years ago by • 0
0
votes
0
replies
924
views
Tutorial: Introduction to Gen3 Webinar
gen3 open-source data-commons big-data
updated 11 days ago by 38k • written 4.1 years ago by ▴ 310
0
votes
0
replies
1.2k
views
Tutorial: VIDEO: Installing BLAST Databases on Your Own Computer
BLAST-databases Linux sequence MacOSX
updated 12 days ago by 38k • written 2.8 years ago by ▴ 440
0
votes
0
replies
2.0k
views
Tutorial: Using OpenEye software for substructure alignments and best-matching low-energy conformer overlays
rmsd alignment openeye
updated 20 days ago by 38k • written 8.7 years ago by ▴ 140
0
votes
1
reply
2.4k
views
Tutorial: Getting the lineage of an organism from NCBI taxonomy data
biosql python taxonomy
updated 12 days ago by 38k • written 4.6 years ago by ▴ 310
0
votes
0
replies
852
views
Tutorial: BrainArray CDF, annotation, etc
db brainarray cdf
updated 12 days ago by 38k • written 2.5 years ago by 84k
117 results • Page 3 of 3
Recent Votes
A: circos plot gene expression by RNA-Seq
Create Interval List for Picard CollectRNASeqmetrics
Answer: multiallelic variants
Answer: LIMMA calculates identical adj.P.Val for different proteins from proteomics
Comment: Hard clip fastq
Answer: Hard clip fastq
Answer: Hard clip fastq
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Recent Replies
Comment: Installing rlang version 1.1.0 by Medha • 0
Password: bQFDPMHbbT I want to install ExomeDepth, these dependencies were not getting installed on its own so I installed it before insta…
Answer: getTable ignores query ranges by Kyle • 0
The short answer is you can theoretically do this you just need to a) make your SNPs are two base-pairs in length (i.e. add 1 to the end) a…
Answer: Installing rlang version 1.1.0 by Lluís R. ★ 1.2k
Having a package duplicated means they are at a different `.libPaths()` sites. Check which version is in which directory and directly remov…
Answer: Somatic truth set by samuel ▴ 180
I think I have found an naswer to my own question. Should anyone have the same question as of March 2023 the relevant data and information…
Answer: GetBM - GERP conservation score for GRCm39 by Kyle • 0
Final solution thanks to Ben's help:: # convert df to Grange. snp_gr <-makeGRangesFromDataFrame(BM_SNPs, seqnames.field = "seqnam…
Comment: GetBM - GERP conservation score for GRCm39 by Kyle • 0
Perfect answer, thanks Ben!
Answer: MapSplice2 gives error if the thread count (-p value) is greater than 2 by vishal.koparde ▴ 10
Any updates??
Comment: how to know what adapter sequences to trim for RNA-seq? by lunarskye222 • 0
Do you happen to know if the middle part of this udi barcode (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCTACATATCTCG) is also part of the TruSeq a…
Comment: Hard clip fastq by GenoMax 127k
If you simply want the reads to be compatible in length then do not adapter trim.
Comment: Hard clip fastq by samuel ▴ 180
@ATpoint, so no adapter trimming first? Just trim the raw fastq?
Answer: Confused on strandedness, what are antisense transcripts? by dsull ★ 4.0k
Think of it on the DNA level: If the mRNA made is the same sequence as the "sense" DNA strand (except U's instead of T's), it is a "sense" …
Comment: Protein name in GenBank by GenoMax 127k
If you must do this programmatically then collect all cases where things differ in order of words (or number of words) like the example abo…
Answer: Hard clip fastq by GenoMax 127k
You can also use `reformat.sh` from [**BBMap suite**][1] as follows reformat.sh -Xmx2g in1=R1.fq.gz in2=R2.fq.gz out1=R1_trim.fq.gz …
Answer: Hard clip fastq by ATpoint 70k
Use `seqtk trimfq`. It makes sense to trim first to your desired length and then run identical downstream processing for a fair comparison.…
Comment: Protein name in GenBank by Mensur Dlakic ★ 23k
I think you either take time to do it properly, or you will end up missing some proteins. BLAST sequence search, even on 1500 genomes, can …
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