User: Rahul

gravatar for Rahul
Rahul30
Reputation:
30
Status:
New User
Location:
India
Last seen:
4 months, 2 weeks ago
Joined:
4 years, 1 month ago
Email:
r*********@gmail.com

Posts by Rahul

<prev • 42 results • page 1 of 5 • next >
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Comment: C: Nextera pair end adapter cleaning
... thank you very much for your comment. After using inbuilt nextera adapters, I got rid of all nextera adapters from lib. But still, it showing illumina universal adapters and solid small RNA adapters in lib. Can you please suggest me the possible trick to remove it. Thanks ...
written 6 months ago by Rahul30
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Nextera pair end adapter cleaning
... Can I use Nextera pair end adapter option in Galaxy Trimmomatic program for cleaning my illumina Nextera 500 transcriptome reads? or else I have to use Netera 500 adapter for cleaning lib. ...
assembly rna-seq written 6 months ago by Rahul30 • updated 6 months ago by Jennifer Hillman Jackson370
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LOCAL BLAST evalue problem
... Hello, I am using local blastx and giving cut off e value of 1.0e-5, but still e value more than 1 is appearing in result.Any suggestions are welcome. blastx -query /home/manish/ncbi/query/SR51.fasta -db /home/manish/ncbi/DB/plazapro2/plazapro2 -out SR51.txt -evalue 1.0e-5 -outfmt 6 -max ...
blast ngs written 22 months ago by Rahul30 • updated 22 months ago by theobroma221.1k
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Comment: C: CEGMA report meaning
... Thanks for your comments.I did not check the contamination.but I will check and remove it. Even I did not cut the starting bases from raw end as there was noise upto 12bp.I tried with cutting 12 bp earlier but the results were very worse. ...
written 2.0 years ago by Rahul30
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Comment: C: CEGMA report meaning
... Actually I have downloaded pair end RNA seq reads SRA349650 for assembly. reads were cleaned by trimmomatics:- adapter cleaning,q20, max read length 30bp. Assembled by Trinity with Group pairs distance- 500 bp,path reinforcement:- 50bp,min legth-200bp, assembled sequences were used for cap3 :- overl ...
written 2.0 years ago by Rahul30
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Comment: C: CEGMA report meaning
... Thanks for your suggestion.I have done busco and got following result. Is there any cut off completeness value for Busco . Completeness Assessment Results: Total # of core genes queried: 429 # of core genes detected Complete: 223 (51.98%) Compl ...
written 2.0 years ago by Rahul30
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Comment: C: CEGMA report meaning
... Thanks for your suggestion.I have done busco and got following result. Is there any cut off completeness value for Busco . Completeness Assessment Results: Total # of core genes queried: 429 # of core genes detected Complete: 223 (51.98%) Compl ...
written 2.0 years ago by Rahul30
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Comment: C: CEGMA report meaning
... is there any ideal cut off completeness value for transcriptome? can we combine complete and partial detected gene and represent.I have got cegma result for transcriptome, but don’t know whether this following result is acceptable. I would be very grateful if you could comment on my problem. COMPLE ...
written 2.0 years ago by Rahul30
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Comment: C: Annotation of repeatative elements
... Dear sir, Thank you very much for your reply.I have assembled the transcriptome of a non-model plant with de Novo assembly method using Trinity, CD-HiT-EST, CAP3. Right now I am looking for the Transposable elements mining in transcriptome data (Including small chunks of TE in protein ...
written 2.6 years ago by Rahul30
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Comment: C: Annotation of repeatative elements
... Dear Sir, I have assembled the transcriptome of a non-model plant with de Novo assembly method using Trinity, CD-HiT-est, CAP3.I have also done with annotation and want to extend my study regarding transposable elements. SSR mining was done with MISA programme. Right now I am trying ...
written 2.6 years ago by Rahul30

Latest awards to Rahul

Popular Question 21 months ago, created a question with more than 1,000 views. For CD-HIT-EST and CAP3
Popular Question 21 months ago, created a question with more than 1,000 views. For RNA seq FASTX quality trimming
Popular Question 21 months ago, created a question with more than 1,000 views. For regarding to Fastqc and SRA file format
Popular Question 21 months ago, created a question with more than 1,000 views. For Kmergenie histogram file
Popular Question 21 months ago, created a question with more than 1,000 views. For SOAP denovo trans
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Mauve Genome Alignment software
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Kmergenie histogram file
Supporter 3.1 years ago, voted at least 25 times.

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