User: amitpande74
amitpande74 • 0
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Posts by amitpande74
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Comment:
C: bowtie2 aligment problems
... How should the command line be:
./bowtie rat/rn4 -s file.fastq test.sam
or should the specific read be specified. I have never used this before so could you kindly help.
...
written 22 days ago by
amitpande74 • 0
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Comment:
C: bowtie2 aligment problems
... 43 base pairs after trimming. The entire read length before trimming is 75bps. ...
written 22 days ago by
amitpande74 • 0
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Comment:
A: bowtie2 aligment problems
... No the reads are single end. This is how the library was prepared. ...
written 22 days ago by
amitpande74 • 0
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... Hi,
I have reads from DNA sequencing,5 pools. The reads look like this:
@NS500455:80:HG7TNBGXB:1:11101:17723:1055 1:N:0:ATCACG
ACTTANGTGTATGTAAACTTCCGACTTCAACTGTATAGGGATCCNAGCTCCAATTCGCCCTATAGTGAGTCGTAT
+
/AAAA#EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE#EEEEEEEEEEEEEEEEEEEEEEEEEE ...
written 23 days ago by
amitpande74 • 0
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... Hi,
I want to download all the files from this archive simultaneously:
ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA166/SRA166615
How can I do this, is there wget command or anything else that might be helpful.
regards,
Amit. ...
written 11 weeks ago by
amitpande74 • 0
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... Hi everyone,
I have ChIP-exo data and I analyzed it both using MACS2 and GEM. The results differ a lot in terms of peaks, over-represented motifs and binding motifs.
Kindly enlighten me as to which one is apt to use.
regards. ...
written 5 months ago by
amitpande74 • 0
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... Hi,
I want to access HMG box TF ChIP seq data In ESC. Tried searching in ENCODE . They have HMG in HepG2 cells.
Can anyone point to a resources please.
Regards,
Amit. ...
written 6 months ago by
amitpande74 • 0
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... 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 7 months ago by
amitpande74 • 0
• updated
7 months ago by
ATpoint ♦ 32k
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Comment:
A: grep DNA after a pattern
... @ lakhujanivijay yes ...
written 7 months ago by
amitpande74 • 0
7
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... 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 7 months ago by
amitpande74 • 0
• updated
7 months ago by
Benn ♦ 7.9k
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Popular Question
2.9 years ago,
created a question with more than 1,000 views.
For extracting reads from BAM files for gene coordinates Tx start Txs end
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