User: debashis.bioinfo

Reputation:
0
Status:
New User
Last seen:
2 years, 3 months ago
Joined:
4 years, 9 months ago
Email:
d***************@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 debashis.bioinfo

<prev • 11 results • page 1 of 2 • next >
0
votes
1
answer
1.2k
views
1
answers
Comment: C: best alignment method
... Raw data are generated from Nexseq 500(2*150). I used different trimming options like trimming reads from 3' end, trimming reads from both 5' and 3' end, convert the reads into 2*100,convert the reads into 2*75, q value > 20, q > 25. This result. I didn't get any specific changes in the mappi ...
written 3.4 years ago by debashis.bioinfo0
0
votes
1
answer
1.2k
views
1
answers
Comment: C: best alignment method
... Thank you for your answer. I have also used Tophat2 but it gives only 55% alignment rate. Can I procede with this mapping percentage? During DEG testing cuffdiff 1.3.0 gives 400 deg and cuffdiff2.2.1 gives 0 deg with this 55% mapping result. ...
written 3.4 years ago by debashis.bioinfo0
7
votes
1
answer
1.2k
views
1
answer
best alignment method
... Hi, I used bowtie for mapping RNA-seq reads to genome. First, I used "--end-to-end" option and got around 77% mapping with genome. Then, I used "--local" option and got 92% mapping with genome. Both of the methods gives different downstream result i.e expression value. Kindly any body suuggest me w ...
rna-seq written 3.4 years ago by debashis.bioinfo0 • updated 3.4 years ago by WouterDeCoster42k
0
votes
1
answer
1.2k
views
1
answers
Comment: C: Maximum Over-Represented Sequence in Bacterial Transcriptome Data
... I used blast. some sequences show similarity with chloroplast genome sequence. But my sequence is from bacteria. Some sequence also show similarity with distant related species of bacteria. Should I remove these reads from fast file before moving toward assembly? ...
written 3.6 years ago by debashis.bioinfo0
1
vote
1
answer
1.2k
views
1
answer
Maximum Over-Represented Sequence in Bacterial Transcriptome Data
... Hi, I have transcriptome data of two sample with paired end chemistry. I have used Trimmomatic and NGS QC Toolkit for quality trimming. But after trimming data there are so many over represented sequence(50 bp length) present in both reads. Can anyone suggest me what procedure should be followed t ...
rna-seq written 3.6 years ago by debashis.bioinfo0 • updated 3.6 years ago by Govardhan Anande130
0
votes
1
answer
1.9k
views
1
answers
Answer: A: Using Sirene in MATLAB for GRN inference
... Hi Diana, I also got the same error. Did you got the solution to your problem? If yes, can you please help me out. Thank you, Debashis ...
written 3.7 years ago by debashis.bioinfo0
0
votes
0
answers
1.2k
views
0
answers
Comment: C: Cufflinks version higher than 1.3.0 gives 0 DEG
... Hello sir, Here I have attached the command and result of both version cufflinks 2.2.1 cufflinks  -p 4 -o cufflinks_control -G gene.gtf aln_sorted.sam RES: Chromosome    Cufflinks    transcript    2417    2680    1000    +    .    gene_id "BG04_4"; transcript_id "AJI20658"; FPKM "198.7189985737" ...
written 3.9 years ago by debashis.bioinfo0
0
votes
0
answers
1.2k
views
0
answers
Cufflinks version higher than 1.3.0 gives 0 DEG
... Hi, I am using Cufflinks 2.2.2(new release) package for differential gene expression analysis between control and treated sample. It gives 0 DEG. Also I try all Cufflinks version higher than 1.3.0 (2012) which gives same result. But when I am using Cufflinks  1.3.0, It gives 3880 DEG.  Please sugg ...
rna-seq written 4.0 years ago by debashis.bioinfo0 • updated 3.3 years ago by Biostar ♦♦ 20
1
vote
1
answer
1.2k
views
1
answer
how to work with sff file generate from roche_454
... Hello all, I want to do the genome assembly. Now I have the sff file generated from roche-454. First, I want to do the quality filteration process and after that I want do the assembly. Please let me know which software will be the best one for low quality base trimming and assembly of the reads. ...
genome written 4.4 years ago by debashis.bioinfo0 • updated 4.4 years ago by rtliu2.0k
0
votes
0
answers
993
views
0
answers
ARACNE algorithm graphics user interface
... Dear All, I want to analyse the microarray data using ARACNE graphic user interface. I follow the tutorial according to the paper published in nature protocol. After inserting all required files, It only shows the "creating index file" dialogue box and does not move ahead. Please help me to solve t ...
software error written 4.7 years ago by debashis.bioinfo0

Latest awards to debashis.bioinfo

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1294 users visited in the last hour