User: debashis.bioinfo
debashis.bioinfo • 0
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Posts by debashis.bioinfo
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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 2.7 years ago by
debashis.bioinfo • 0
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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 2.7 years ago by
debashis.bioinfo • 0
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... 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 ...
written 2.7 years ago by
debashis.bioinfo • 0
• updated
2.7 years ago by
WouterDeCoster ♦ 37k
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... 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 2.9 years ago by
debashis.bioinfo • 0
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... 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 ...
written 2.9 years ago by
debashis.bioinfo • 0
• updated
2.9 years ago by
Govardhan Anande • 130
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... 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 3.0 years ago by
debashis.bioinfo • 0
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... 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 3.2 years ago by
debashis.bioinfo • 0
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... 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 ...
written 3.2 years ago by
debashis.bioinfo • 0
• updated
2.6 years ago by
Biostar ♦♦ 20
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... 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.
...
written 3.7 years ago by
debashis.bioinfo • 0
• updated
3.7 years ago by
rtliu • 2.0k
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... 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 ...
written 4.0 years ago by
debashis.bioinfo • 0
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