User: amitpande74
amitpande74 • 0
- Reputation:
- 0
- Status:
- New User
- Last seen:
- 2 days, 3 hours ago
- Joined:
- 7 years, 3 months ago
- Email:
- a**********@gmail.com
Profile information, website and location are not shown for new users.
This helps us discourage the inappropriate use of our site.
Posts by amitpande74
<prev
• 9 results •
page 1 of 1 •
next >
3
votes
1
answer
81
views
1
answer
... Hi everyone,
I have used bedtools bamtobed to extract information. My file looks like this:
chr10 1195932 1195977 NB551726:5:H2HT5BGXC:1:11101:11237:5492 41 +
chr10 1195932 1195977 NB551726:5:H2HT5BGXC:1:11101:22230:17587 41 +
I am loosing the strand information when I tried bedtools mer ...
written 11 days ago by
amitpande74 • 0
• updated
11 days ago by
ATpoint ♦ 23k
0
votes
1
answer
129
views
1
answers
Comment:
A: grep DNA after a pattern
... @ lakhujanivijay yes ...
written 26 days ago by
amitpande74 • 0
7
votes
1
answer
129
views
1
answer
... HI,
I have DNA sequences like these :
and I want to keep all sequences after this pattern "ACTTAAGTGTATGTAAACTTCCGACTTCAACTG" beginning with "TA". I tried
grep -v "ACTTAAGTGTATGTAAACTTCCGACTTCAACTG" file.txt
but it does not work.
Kindly help.
...
written 26 days ago by
amitpande74 • 0
• updated
26 days ago by
Benn ♦ 7.7k
0
votes
1
answer
266
views
1
answer
... Hi,
I want to analyze RNAseq data for detecting Chimeric transcripts. Which tool would be best to use. I am aware of some from here [Nature][1].
Kindly help.
thanks.
[1]: https://www.nature.com/articles/srep21597 ...
written 10 months ago by
amitpande74 • 0
• updated
10 months ago by
enxxx23 • 230
0
votes
1
answer
551
views
1
answers
Comment:
C: cutadapt error problem
... >barcode01
CGCAGG
>barcode02
CTCTGCA
>barcode03
CCTAGGT
>barcode04
GGATCAA
>barcode05
GCAAGAT
>barcode06
ATGGAGA
>barcode07
CTCGATG
>barcode08
GCTCGAA ...
written 11 months ago by
amitpande74 • 0
• updated
11 months ago by
Devon Ryan ♦ 92k
0
votes
1
answer
551
views
1
answers
Comment:
A: cutadapt error problem
... Thanks for your replies.....kindly look [here]([https://cutadapt.readthedocs.io/en/stable/guide.html#named-adapters)
I tried using it without cd but yet it complains about too many arguments.
cutadapt -a TCGCAGGACC -a CTCTGCAACC -a CCTAGGTACC -a GGATCAAACC -a GCAAGATACC -a ATGGAGAACC -a CTCGA ...
written 11 months ago by
amitpande74 • 0
• updated
11 months ago by
Devon Ryan ♦ 92k
1
vote
1
answer
551
views
1
answer
... Hi,
I am trying to use cutadapt installed from conda.
I am running this command :
cutadapt -a cd /media/moloy/LaCie/bburg/20180910_FMT-IBS-Exp1/unzipped/barcodes.fasta -o cd /media/moloy/LaCie/bburg/20180910_FMT-IBS-Exp1/output.fastq input cd /media/moloy/LaCie/bburg/20180910_FMT-IBS-Exp1/unz ...
written 11 months ago by
amitpande74 • 0
1
vote
1
answer
827
views
1
answer
... Hi,
I have FPKM values for 1000 genes and would like the classify these based on FPKM values as high, medium and low expressed. Can someone kindly tell me how to do this using R. ...
written 2.4 years ago by
amitpande74 • 0
• updated
2.4 years ago by
mmmmcandrew • 70
2
votes
3
answers
2.0k
views
3
answers
... Hi,
I have a list of Refseq annotated gene coordinates and I would like to extract the reads for the same in one go. I have read many posts here and at Seqanswers, but those are restricted to a particular region. for example samtools view input.bam "Chr10:18000-45500" > output.bam.
How ca ...
written 4.5 years ago by
amitpande74 • 0
• updated
4.5 years ago by
Alex Reynolds ♦ 28k
Latest awards to amitpande74
Popular Question
2.4 years ago,
created a question with more than 1,000 views.
For extracting reads from BAM files for gene coordinates Tx start Txs end
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 884 users visited in the last hour