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18 results • Page
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Showing top results for tag:
bedFile
•
reset
1
vote
4
replies
174
views
exon.bed file for coverage
bedtools
NGS
bedFile
coverage
7 days ago by
Sabeen
• 0
0
votes
3
replies
294
views
Handing scafflold names for plink bed file
plink
bedfile
snp
genome
updated 17 days ago by
rs146
• 0 • written 6 months ago by
nitinra
▴ 10
0
votes
4
replies
1.4k
views
Clustering and Bedtools
clustering
bedtools
bedfile
updated 13 months ago by
Biostar
20 • written 3.8 years ago by
user_g
▴ 20
0
votes
2
replies
648
views
targets in a bed at or above a coverage
250x
bedfile
bam
updated 21 months ago by
harold.smith.tarheel
★ 4.6k • written 21 months ago by
bioguy24
▴ 220
0
votes
0
replies
1.3k
views
TruSeq Exome Kit bed file old version
whole-exome-sequencing
bedfile
3.5 years ago by
fbrundu
▴ 300
5
votes
1
reply
976
views
append to column in bedfile
bedfile
file formating
updated 4.2 years ago by
Devon Ryan
98k • written 4.2 years ago by
a.rex
▴ 250
2
votes
2
replies
1.1k
views
tab-delimited file - use in bedtools?
bedtools
tab-delimited file
bedfile
updated 4.4 years ago by
michael.ante
★ 3.6k • written 4.4 years ago by
a.rex
▴ 250
3
votes
1
reply
1.9k
views
Finding downstream Gene Closest To A Given Location
bedtools
closest
gene
bedfile
updated 4.4 years ago by
harold.smith.tarheel
★ 4.6k • written 4.4 years ago by
PAn
▴ 20
3
votes
4
replies
1.1k
views
generating midpoints on a bedfile
bedtools
bedfile
midpoint
updated 4.5 years ago by
WouterDeCoster
45k • written 4.5 years ago by
a.rex
▴ 250
7
votes
7
replies
2.4k
views
How to sort chromosome name in bed file
Chrmosome
bedfile
sort
updated 4.8 years ago by
GenoMax
99k • written 4.8 years ago by
raya.girish
▴ 20
1
vote
5
replies
1.0k
views
Generate bed co-ordinates other then given input bed file
bedfile
bedtools
updated 4.9 years ago by
A. Domingues
★ 2.5k • written 4.9 years ago by
Chirag Parsania
★ 1.9k
1
vote
2
replies
1.7k
views
Interpreting bed file...
bedfile
bamfile
gff
updated 5.1 years ago by
michael.ante
★ 3.6k • written 5.1 years ago by
ab.tsubaki
▴ 50
0
votes
2
replies
3.4k
views
how to extract the variants using Bed file
next-gen
sequencing
bedfile
variant_calling
updated 5.2 years ago by
christopher medway
▴ 450 • written 5.2 years ago by
k.manojkumar2991
▴ 10
0
votes
1
reply
1.2k
views
java parser for bed file
bedFile
java
5.4 years ago by
alex
▴ 230
3
votes
7
replies
1.5k
views
Regarding PCR duplicates vs duplicate entries in a bedfile
bedfile
duplicates
pcr
updated 5.4 years ago by
Antonio R. Franco
★ 4.6k • written 5.4 years ago by
eudoraleer
▴ 10
2
votes
3
replies
1.7k
views
Count total base pairs in bedfile B that overlap bedfile A
bedtools
cnv
bedfile
bed
updated 5.5 years ago by
Alex Reynolds
32k • written 5.5 years ago by
QVINTVS_FABIVS_MAXIMVS
★ 2.4k
10
votes
7
replies
7.7k
views
BedTools IntersectBed resulting in Segmentation Fault with BedFile
bedtools
intersectbed
bedfile
vcf
updated 6.3 years ago by
dariober
12k • written 6.3 years ago by
ali
• 0
0
votes
5
replies
1.4k
views
Tool to calculate extreme most positions in a bed file for a given window
bedfile
updated 6.4 years ago by
Alex Reynolds
32k • written 6.5 years ago by
Aishwarya Kulkarni
▴ 80
18 results • Page
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Recent Votes
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Comment: A simple tutorial for a complex ComplexHeatmap
Comment: A simple tutorial for a complex ComplexHeatmap
Answer: Hunting invisible characters?
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Recent Replies
Comment: How can I Extract Transposable element from a new genome assembly?
by
Philipp Bayer
6.9k
if you can transform the bed to gff (galaxy has tools for that), you could also use liftoff which wraps all of this in a pipeline https://g…
Comment: A simple tutorial for a complex ComplexHeatmap
by
Rob
▴ 40
Great! Thank you ATpoint
Comment: Hunting invisible characters?
by
seidel
7.6k
Another way to see hidden characters is to pipe them through octal dump: `cat infile | od -c` this will print out hidden characters, newlin…
Comment: How can I Extract Transposable element from a new genome assembly?
by
GenoMax
99k
Align your assemblies to each other using an aligner like `lastz` ([**LINK**][1]). You could also use `blat` if you are sure the assemblies…
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by
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99k
It is going to take as long as it takes. You need to be patient and wait until the prompt returns. Based on speed of your CPU/disk things c…
Comment: Hunting invisible characters?
by
GenoMax
99k
You could have looked at the file using `cat -vet` which would have shown all characters in the file. Printable and non.
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avelarbio46
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I'm not sure about three things: What does -M and -O do exactly that could benefit in my case? Why should I specify -t if I don't necessa…
Comment: Hunting invisible characters?
by
geneticatt
▴ 120
Thank you, using `dos2unix` worked perfectly!
Answer: Hunting invisible characters?
by
Mensur Dlakic
★ 10k
You may want to read [**this**][1]. I think you may be able to fix your adaper file by typing: dos2unix i5R.txt If an error pops …
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32k
Please do not delete posts that have comments/answers.
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Is there a way to extract ICE bias from balanced .cool file? I know that you can find weight associated with each bin by `cooler dump --bal…
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Yeah, miRNA could be only verified in wet-lab. Take a look at [stem-loop PCR][1]. I've used it and it works really well. [1]: https://j…
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by
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32k
Because this is a plain copy-paste from the novogene page, it has numbers (pointers to specific references that the source has), but not th…
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Mensur Dlakic
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This is correct. `X` means any amino acid. Most substitution matrices apply identical penalty (`-1`) when any amino-acid is aligned with X …
Answer: differential expression analysis
by
Mensur Dlakic
★ 10k
I think the numbers you cite are the most extreme values that people will still accept. In most cases I would go for lower p-values (at lea…
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