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226
votes
39
replies
282k
views
33 follow
Gene Id Conversion Tool
mapping conversion
updated 9 months ago by 39k • written 13.6 years ago by ▴ 620
65
votes
3
replies
274k
views
Understanding up and down regulated genes from LOG2 foldchange or foldchange
protein gene-expression RNA-Seq
updated 3 months ago by 39k • written 9.0 years ago by ▴ 960
267
votes
29
replies
257k
views
25 follow
How To Filter Mapped Reads With Samtools
samtools
updated 6 months ago by 39k • written 10.6 years ago by ▴ 610
323
votes
90
replies
219k
views
57 follow
Tools To Calculate Average Coverage For A Bam File?
coverage bam sequencing
updated 8 months ago by 39k • written 12.4 years ago by 4.9k
43
votes
24
replies
196k
views
25 follow
How To Update R In Ubuntu ?
r ubuntu
updated 14 months ago by ▴ 50 • written 9.5 years ago by ▴ 210
62
votes
14
replies
186k
views
9 follow
How To Deal With Duplicate Row Names Error In R
r
updated 5 weeks ago by 11k • written 10.3 years ago by ▴ 900
12
votes
6
replies
183k
views
How can I uninstall my packages in Rstudio
R Bioconductor
updated 2.8 years ago by 11k • written 5.4 years ago by ▴ 40
118
votes
31
replies
180k
views
17 follow
Correct Way To Parse A Fasta File In Python
fasta parsing python
updated 20 months ago by 129k • written 13.1 years ago by 11k
151
votes
42
replies
176k
views
22 follow
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
heatmap r
updated 12 months ago by 39k • written 11.3 years ago by 20k
126
votes
19
replies
173k
views
13 follow
What'S The Difference Between Cds And Orf?
cds orf
updated 2.1 years ago by • 0 • written 11.0 years ago by ▴ 350
277
votes
39
replies
168k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA bam GEO
updated 10 weeks ago by 39k • written 8.8 years ago by 20k
193
votes
21
replies
166k
views
12 follow
Forward And Reverse Strand Conventions
sequence strand
updated 6 months ago by 98k • written 12.6 years ago by ★ 2.8k
142
votes
14
replies
165k
views
16 follow
What Is The Sequencing 'Depth' ?
next-gen sequencing
updated 3.5 years ago by ★ 2.1k • written 13.2 years ago by 154k
122
votes
11
replies
161k
views
11 follow
How Can I Convert Bam To Sam?
next-gen sequencing bam sam conversion
updated 21 months ago by • 0 • written 12.9 years ago by 4.9k
135
votes
18
replies
158k
views
16 follow
Blast - Formatting Output
blast format output
updated 5 months ago by ▴ 20 • written 9.5 years ago by ▴ 320
161
votes
8
replies
157k
views
Generate vcf.gz file and its index file vcf.gz.tbi
vcf tabix
updated 10 months ago by 39k • written 10.5 years ago by ▴ 430
360
votes
81
replies
138k
views
34 follow
Tool: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel next-gen ngs
6 weeks ago by ole.tange ★ 4.3k
224
votes
38
replies
136k
views
29 follow
Tool: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
genome coordinates conversion liftover ensembl Tool
updated 5 months ago by ▴ 90 • written 10.3 years ago by 19k
91
votes
39
replies
134k
views
19 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 6 weeks ago by ▴ 120 • written 10.9 years ago by ▴ 370
10
votes
4
replies
133k
views
How To Count The Number Of Elements In A Column Other Than 'X' In R
r programming
updated 11.9 years ago by 4.4k • written 11.9 years ago by ▴ 20
143
votes
30
replies
128k
views
25 follow
Useful Bash Commands To Handle Fasta Files
command-line command-line fasta list bash
updated 8 months ago by 39k • written 11.3 years ago by ★ 2.9k
129
votes
32
replies
123k
views
29 follow
Is There A Free Alternative To Ingenuity Pathway Analysis?
network pathway
updated 14 months ago by 39k • written 12.3 years ago by ▴ 530
23
votes
9
replies
122k
views
8 follow
How to calculate "fold changes" in gene expression?
R gene
updated 3 months ago by 39k • written 8.1 years ago by ▴ 70
26
votes
10
replies
121k
views
Calculating P-Values From Z-Scores
statistics r
updated 11 months ago by 39k • written 11.3 years ago by ▴ 900
13
votes
8
replies
121k
views
7 follow
Convert A Text File Into A Fasta File
fasta
updated 8 months ago by 39k • written 11.6 years ago by ▴ 520
160
votes
52
replies
119k
views
28 follow
Fastq Convert To Fasta
perl
9.6 years ago by biolab ★ 1.4k
119
votes
25
replies
119k
views
12 follow
Where Can I Download Human Reference Genome In Fasta Format? Hgref.Fa File
human fasta sequence bwa
updated 6.3 years ago by ▴ 160 • written 12.9 years ago by 4.9k
98
votes
9
replies
115k
views
11 follow
How To Merge Two Fastq.Gz Files?
merge fastq
updated 13 months ago by ▴ 40 • written 9.7 years ago by ▴ 750
3
votes
3
replies
114k
views
Find mismatch in two columns in a data frame in R
R
updated 7.2 years ago by ▴ 10 • written 7.2 years ago by ▴ 20
744
votes
162
replies
114k
views
101 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 5 weeks ago by 1.8k • written 6.5 years ago by 98k
46
votes
10
replies
112k
views
8 follow
Which Expression Units To Use, Fpkm Or Rpkm ?
fpkm rpkm rna-seq
updated 5 months ago by 39k • written 10.2 years ago by ★ 1.5k
115
votes
21
replies
111k
views
14 follow
When To Choose Python Over Perl (And Vice Versa)?
python perl comparison
updated 11.2 years ago by ▴ 30 • written 11.6 years ago by ★ 2.6k
63
votes
16
replies
109k
views
11 follow
from .BAM to .BAI using samtools
sequencing samtools next-gen
updated 16 months ago by 39k • written 8.7 years ago by ▴ 860
118
votes
7
replies
108k
views
Bam And Indexed Bam Files
bam index
11.4 years ago by Sahel ▴ 260
91
votes
10
replies
106k
views
11 follow
Best Way To Do Pathway Analysis Of A Set Of Genes?
protein genes pathway analysis function
updated 11.2 years ago by ★ 2.6k • written 11.2 years ago by ★ 1.0k
28
votes
8
replies
105k
views
7 follow
How To Calculate Fpkm (Fragments Per Kilobase Of Exon Per Million Fragments Mapped)
rna fpkm rpkm
written 12.2 years ago by ▴ 210
73
votes
25
replies
102k
views
14 follow
How to count fastq reads
sequence next-gen fastq reads
updated 11 months ago by 39k • written 8.1 years ago by ▴ 250
118
votes
15
replies
102k
views
15 follow
Economics Of A Career In Bioinformatics
career
updated 12.4 years ago by • 0 • written 12.6 years ago by ▴ 210
100
votes
15
replies
100k
views
15 follow
Convertion Of Gff3 To Gtf
gtf gff
updated 3 months ago by ▴ 20 • written 11.0 years ago by 12k
98
votes
31
replies
100k
views
20 follow
How To Split A Bam File By Chromosome
bam split chromosome
updated 15 months ago by ▴ 120 • written 11.0 years ago by ▴ 390
63
votes
9
replies
97k
views
10 follow
Blog: Gene expression units explained: RPM, RPKM, FPKM and TPM
gene-expression RNA-Seq
updated 3 months ago by 39k • written 5.7 years ago by ★ 2.1k
31
votes
8
replies
96k
views
8 follow
How Do You Start Writing An Algorithm? Help Needed!
java structure algorithm
updated 12.4 years ago by • 0 • written 13.1 years ago by ▴ 70
277
votes
33
replies
94k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 3 months ago by 39k • written 9.6 years ago by 20k
120
votes
53
replies
90k
views
22 follow
How to plot coverage and depth statistics of a bam file
bam coverage depth next-gen-sequencing
updated 11 weeks ago by • 0 • written 9.0 years ago by ▴ 330
173
votes
30
replies
89k
views
17 follow
What Is The Best Method To Find Orthologous Genes Of A Species?
orthologues
updated 16 months ago by 39k • written 12.1 years ago by ▴ 610
97
votes
19
replies
89k
views
12 follow
How To Get The Sequence Of A Genomic Region From Ucsc?
sequence ucsc fasta
updated 9 months ago by 39k • written 13.3 years ago by 27k
39
votes
8
replies
88k
views
samtools sorting and indexing
samtools index sort
updated 3.4 years ago by ▴ 320 • written 5.9 years ago by ▴ 80
167
votes
41
replies
88k
views
27 follow
Multiline Fasta To Single Line Fasta
sequence fasta
updated 4 months ago by • 0 • written 12.0 years ago by ▴ 240
70
votes
16
replies
86k
views
12 follow
What Does Samtools Flagstat Results Mean?
rna samtools mouse
updated 14 months ago by 154k • written 11.7 years ago by ▴ 510
84
votes
16
replies
86k
views
9 follow
Number of mapped reads from BAM file
bam sam reads mapping
updated 6 months ago by ▴ 50 • written 8.1 years ago by ★ 2.6k
1,000 results • Page 1 of 20
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Answer: How to calculate TPM from featureCounts output
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A: How To Predict Pseudogenes In A Genome
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How To Predict Pseudogenes In A Genome
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Recent Replies
Answer: Getting species names and taxa id from assembly accession number by MirianT_NCBI ▴ 580
Hi, As an alternative, you could use [NCBI Datasets][1] for this task. NCBI Datasets allows users to retrieve metadata reports in JSON or…
Comment: Optimum setting for local blastp for ~10K sequences by sodiumnitrate ▴ 20
Thank you for the info! It turned out that running all 10k at once is actually faster than running one or two at a time!
Answer: Installation of PPFinder by GenoMax 129k
Since the software is still [**listed on the Brent lab**][1] website your best bet would be to email the investigator and ask that they fix…
Comment: How to calculate TPM from featureCounts output by rpolicastro 12k
If you want to go that route, yes.
Comment: Difference between USCS exon coordinates and ensembl by ATpoint 72k
What did you download from UCSC? 1-off usually means one file is zero-based and the other 1-based. BED files from UCSC are 0-based, Ensembl…
Comment: Alignment of case vs. control from different origin by sativus • 0
Thank you kindly for the explanation, it is highly appreciated. I suppose i was a bit confused as you quite often see people validating the…
Answer: Gene enrichment analysis by nux ▴ 10
Hello. For this you have to select 'hyper' as your method and then provide a complete list of genes which both include the candidate and no…
Comment: CNNScoreVariants Error by bestone ▴ 10
Thank you for replying I updated it worked but it gives another Error A USER ERROR has occurred: Invalid argument ' -V'.
Comment: Impute haplotypes (ImputePipelinePlugin) execution error - PHG by jrodrigu • 0
Thank you so much. I made the suggested changes. However, I still have the same problem. Please check the new log file. https://github.c…
Comment: Getting same value for start and end position, "DNA methylation" by ATpoint 72k
That's a comment, not an answer, please use `ADD COMMENT`.
Comment: Getting same value for start and end position, "DNA methylation" by bioinfo_ga ▴ 50
Are you working on bisulphite kind of data or chipseq ????
Answer: How to calculate TPM from featureCounts output by bioinfo_ga ▴ 50
hi , You can use a python package rnanorm [https://pypi.org/project/rnanorm/]. The input required are your read count values from feature …
Comment: How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by by biofalconch ▴ 580
Hey, if you arelady have the barcodes, you could use samtools `samtools view -h -b -f CB:Z:TAAGAGATCCTATGTT > TAAGAGATCCTATGTT.bam` Hope…
Answer: How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by by biofalconch ▴ 580
Here is a code that should work, but just like everyone else in the comments I'm a little confused why would you need to separate them: …
Comment: Make a BedGraph file by kirillkirilenko ▴ 10
It works, thank you!
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