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238
votes
176
replies
84k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 5 months ago by 38k • written 7.6 years ago by ★ 4.6k
84
votes
16
replies
84k
views
9 follow
Number of mapped reads from BAM file
bam sam reads mapping
updated 4 months ago by ▴ 50 • written 7.9 years ago by ★ 2.6k
99
votes
31
replies
81k
views
18 follow
Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
bam picard samtools merge
updated 8 months ago by 38k • written 11.7 years ago by ★ 5.0k
79
votes
22
replies
81k
views
16 follow
How To Split One Big Sequence File Into Multiple Files With Less Than 1000 Sequences In A Single File
next-gen sequencing fasta rna r perl
updated 4 months ago by 38k • written 11.4 years ago by ▴ 290
106
votes
45
replies
80k
views
30 follow
How To Extract A Sequence From A Big (6Gb) Multifasta File ?
fasta
updated 6 months ago by ▴ 20 • written 10.7 years ago by ▴ 320
70
votes
20
replies
80k
views
15 follow
How To Get Ensembl Id (Gene, Transcript, Protein) Mapping Information?
ensembl identifiers mapping
updated 11 weeks ago by 38k • written 12.4 years ago by ▴ 180
55
votes
11
replies
79k
views
8 follow
merge large amount of fastq files into a single one
ChIP-Seq fastq
updated 9 months ago by 38k • written 8.0 years ago by ▴ 220
185
votes
43
replies
78k
views
29 follow
Drawing Chromosome Ideograms With Data
chromosome visualization ideogram
updated 6 months ago by 38k • written 13.0 years ago by ★ 1.6k
120
votes
8
replies
77k
views
GRCh37/38(NCBI) vs hg19/hg38(UCSC)
ncbi ucsc grch38 hg38
updated 14 months ago by 38k • written 8.5 years ago by ▴ 520
33
votes
4
replies
76k
views
7 follow
Merging Bam Files
picard samtools
updated 3.8 years ago by ▴ 60 • written 11.2 years ago by ▴ 180
136
votes
25
replies
75k
views
14 follow
Tutorial: Piping With Samtools, Bwa And Bedtools
unix samtools bwa bedtools
updated 11 months ago by 38k • written 10.9 years ago by ★ 4.2k
99
votes
16
replies
75k
views
15 follow
How Much Coverage Do We Need For An Rna-Seq Experiment?
rna-seq coverage
8.3 years ago by Obi Griffith 20k
126
votes
24
replies
74k
views
18 follow
Sequence Length Distribution From A Fastq File
sequence length fastq
updated 3.9 years ago by • 0 • written 9.8 years ago by ▴ 360
157
votes
62
replies
74k
views
37 follow
Selecting Random Pairs From Fastq?
random fastq sequence illumina code
updated 9 months ago by • 0 • written 12.0 years ago by 4.1k
94
votes
25
replies
74k
views
20 follow
Extract Sub-Set Of Regions From Vcf File
vcf tabix genome filter
updated 11 days ago by 2.6k • written 10.8 years ago by ▴ 820
15
votes
12
replies
73k
views
8 follow
BLAST Database error: No alias or index file found for nucleotide database
blast blastn sift makeblastdb
updated 7 months ago by • 0 • written 8.4 years ago by ▴ 310
103
votes
12
replies
71k
views
7 follow
Bedtools Compare Multiple Bed Files?
bedtools intersect
updated 5 months ago by 38k • written 11.4 years ago by ★ 1.7k
20
votes
2
replies
71k
views
Subsetting in R based on row name?
R
updated 7.0 years ago by 103k • written 7.0 years ago by ▴ 80
81
votes
21
replies
71k
views
13 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 5 weeks ago by ★ 2.9k • written 4.7 years ago by ▴ 530
43
votes
25
replies
70k
views
10 follow
Will A Masters In Bioinformatics Help Me In Getting A Job?
career education
updated 12.0 years ago by ★ 1.4k • written 12.0 years ago by ▴ 50
122
votes
17
replies
70k
views
8 follow
What Are Phased And Unphased Genotypes?
genotyping genome
updated 12 months ago by 38k • written 11.9 years ago by ▴ 370
235
votes
45
replies
69k
views
34 follow
What Is The Best Pipeline For Human Whole Exome Sequencing?
next-gen sequencing illumina exome human
updated 11.8 years ago by ▴ 50 • written 12.8 years ago by 4.8k
67
votes
18
replies
69k
views
17 follow
Project For A Beginner Bioinformatics Student
project java
updated 8 months ago by 38k • written 11.4 years ago by ▴ 230
33
votes
17
replies
69k
views
14 follow
How To Draw A Heat Map For Gene Expression Data?
microarray heatmap
updated 9 weeks ago by 38k • written 11.8 years ago by ▴ 80
22
votes
2
replies
69k
views
How Can I Make A Bed File?
bed
updated 11.5 years ago by ▴ 260 • written 11.5 years ago by ▴ 580
40
votes
14
replies
68k
views
9 follow
Synonymous And Non-Synonymous Snps
snp
updated 10 months ago by 38k • written 12.2 years ago by ▴ 250
194
votes
44
replies
68k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 10 weeks ago by 38k • written 10.5 years ago by 20k
188
votes
50
replies
67k
views
41 follow
How To Remove The Same Sequences In The Fasta Files?
fasta sequence duplicates
updated 5 months ago by 38k • written 12.4 years ago by ▴ 340
138
votes
21
replies
67k
views
18 follow
Database Of Tumor Suppressors And/Or Oncogenes
cancer gene database oncogene tumor
2.5 years ago by Malachi Griffith 19k
59
votes
15
replies
67k
views
9 follow
BAM/SAM to FASTA conversion
sam bam
updated 11 months ago by 38k • written 8.1 years ago by ★ 1.4k
24
votes
23
replies
67k
views
7 follow
Multiple Histograms In One Plot
r
updated 15 months ago by 38k • written 9.8 years ago by ★ 1.8k
1
vote
2
replies
67k
views
"SyntaxError: unexpected EOF while parsing " IN PYTHON 3.7
PYTHON
updated 24 months ago by 97k • written 2.9 years ago by • 0
74
votes
13
replies
65k
views
10 follow
Tutorial: Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r cancer classification
updated 4 months ago by 38k • written 9.3 years ago by ★ 1.2k
40
votes
15
replies
65k
views
14 follow
Converting Affymetrix Probes To Gene Ids
affymetrix conversion entrez
updated 5 months ago by 38k • written 9.7 years ago by ▴ 140
19
votes
8
replies
64k
views
6 follow
Pheatmap Annotation
r heatmap
updated 7.6 years ago by ▴ 550 • written 10.0 years ago by ▴ 80
51
votes
18
replies
64k
views
10 follow
Extract User Defined Region From An Fasta File
sequence fasta
updated 5.7 years ago by ▴ 30 • written 11.7 years ago by ▴ 290
111
votes
25
replies
64k
views
14 follow
Is My Bam File Sorted ?
bam next-gen sequencing sort
updated 6 weeks ago by ▴ 10 • written 12.1 years ago by 153k
35
votes
9
replies
64k
views
8 follow
Minor allele frequency calculation
SNP next-gen
updated 10 months ago by 38k • written 8.4 years ago by ▴ 50
20
votes
15
replies
63k
views
12 follow
Python Script To Translate Rna Sequences To Protein Sequences
python biopython translation
updated 9.5 years ago by ▴ 50 • written 12.4 years ago by ▴ 70
53
votes
10
replies
63k
views
6 follow
Fold change - a final explanation
RNA-Seq
updated 2.6 years ago by • 0 • written 4.5 years ago by ▴ 320
51
votes
15
replies
62k
views
15 follow
Any Recommendations For Software For Drawing Plasmid Maps?
visualization software
updated 11 months ago by 38k • written 11.8 years ago by ▴ 70
40
votes
7
replies
62k
views
Clustering Data (Rna-Seq) Using R To Produce A Heatmap
r rna heatmap clustering gene
updated 9 months ago by 38k • written 11.4 years ago by ▴ 450
50
votes
15
replies
62k
views
12 follow
Sequence Number Count In Fastq.Gz File
counts sequence fastq
updated 6 weeks ago by 38k • written 11.7 years ago by ★ 1.7k
53
votes
4
replies
61k
views
What is difference between soft-clipped and hard-clipped in SAM specification?
sequence next-gen-sequencing
updated 5 months ago by 38k • written 8.4 years ago by ▴ 800
25
votes
5
replies
61k
views
7 follow
Rpkm Calculation For Genes
rpkm rna-seq
updated 10.4 years ago by 13k • written 10.4 years ago by ▴ 270
36
votes
14
replies
60k
views
9 follow
What Is The Difference Between Hg18 And Hg19?
genome hg hg
updated 11.1 years ago by 14k • written 11.1 years ago by ▴ 170
102
votes
30
replies
59k
views
25 follow
Tools To Find Gene Ontology Term Enrichment
gene enrichment tool
updated 8 months ago by 38k • written 13.0 years ago by ★ 1.0k
8
votes
6
replies
59k
views
How To Calculate Coverage
fastq coverage
updated 9.2 years ago by ▴ 90 • written 9.2 years ago by ★ 1.2k
152
votes
24
replies
59k
views
19 follow
Recommended Tools For Alternative Splicing Detection From Rna-Seq Data
splicing tools rna-seq alternative-splicing
updated 8 months ago by 38k • written 10.1 years ago by 10k
361
votes
57
replies
59k
views
43 follow
Forum: Recommend Your Favorite Bioinformatics Books
books education
updated 6 months ago by 84k • written 13.1 years ago by 97k
1,000 results • Page 2 of 20
Recent Votes
Answer: Cellranger sequencing
Answer: Using STAR for RNA seq-alignment.
Answer: Download Specific Individuals From Dbsnps?
blastn command line returning empty file
C: The Biostar Handbook. A bioinformatics e-book for beginners.
A: What Makes One Probability Distribution Better For Rna-Seq Than Another?
Answer: How to demultiplex single end - dual index run - NextSeq 500
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Scholar to GenoMax 127k
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Recent Replies
Comment: chloroplast genome gaps by ugur • 0
after alignment, it occurs in different sizes of gaps
Answer: Cellranger sequencing by ATpoint 70k
Not that I am aware of. Unlike methods such as salmon it does genome alignment and does not resolve the exact transcript expression composi…
Answer: Assembly at lineage level from shotgun data ? by Mensur Dlakic ★ 23k
The paper I list below is meant for improving the existing MAG assemblies. Yet the program will do what you want: if you give it a referenc…
Comment: Ortholog assembly and extraction by GenoMax 127k
Many seem to use `orthofinder` for this purpose. See if it is useful: https://github.com/davidemms/OrthoFinder
Answer: Python formatting when visualizing Primer3-py dimers by Wayne ★ 1.6k
Try this so you'll see that using [tabulate](https://github.com/astanin/python-tabulate) to print the dataframe causes it to respect the li…
Comment: Python formatting when visualizing Primer3-py dimers by bhumm ▴ 30
Glad I am making this more clear. The 'test1' in practice will be the 'primer name' to allow for tracking of other metrics (Tm, hairpin str…
Comment: Python formatting when visualizing Primer3-py dimers by Wayne ★ 1.6k
Starting to understand what you want and why. My question is now also then do you actually want the brackets? They seem to shift the rela…
Comment: Python formatting when visualizing Primer3-py dimers by bhumm ▴ 30
Hi Wayne, Thanks for the response. I have updated the code to be more representative of the toy example I have provided - apologies for an…
Comment: chloroplast genome gaps by Pierre Lindenbaum 153k
> , but the alignment results show different size gaps. what does it mean ?
Comment: lncTar by Ram 38k
I see that you added an answer to a 2 year old post. Don't do that - what you added was "I have this problem too" comment, not an answer. I…
Comment: LncTar error by Ram 38k
Do not add answers unless you're answering the top level question. Given that you've opened a new question, I'm deleting this post.
Comment: Samtools fixmate: whta's wrong with the terminal? by Ram 38k
Lol I started writing first, then discovered each issue as I was writing. All I saw was the `-0` but then oh my goodness, so many problems!
Comment: SKAT in R by Pierre Lindenbaum 153k
cross-posted: https://bioinformatics.stackexchange.com/questions/20772
Comment: Samtools fixmate: whta's wrong with the terminal? by Pierre Lindenbaum 153k
oh , Ram was too fast ! :-D
Answer: Samtools fixmate: whta's wrong with the terminal? by Pierre Lindenbaum 153k
1) your [standard][1] output is redirected to the terminal instead of a [file][2]. 2) there is no such option `-0` (zero) . your want …
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