User: bilal.sarwar

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bilal.sarwar10
Reputation:
10
Status:
New User
Location:
Pakistan/Lahore/CEMB-PU
Last seen:
1 year, 4 months ago
Joined:
4 years, 3 months ago
Email:
b***********@cemb.edu.pk

Posts by bilal.sarwar

<prev • 11 results • page 1 of 2 • next >
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Answer: A: Kissplice: Problem getting SNPs in test data
... hello leandro I am facing long runtime to prepare the KisSplice output file for KisSplice2rwfTranscriptome run. I used -s=1 switch too. please guide me how to solve this issue? you wrote in your above answer (possibly coupled with the --experimental option, if you are facing long runtimes). ...
written 2.1 years ago by bilal.sarwar10
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Comment: C: Help required to Rectify/reformat the fasta header of nr database fasta sequence
... bro, I got an error while preparing the blastable database after Rectify the fasta headers with -parse_seqids tag. without -parse_seqids all work well. actually, i am using Blast2Go software for mapping and annotation. here in this page [How to create a Fasta file database for local Blast and to im ...
written 3.5 years ago by bilal.sarwar10
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Comment: C: Help required to Rectify/reformat the fasta header of nr database fasta sequence
... thanks for help ..... :) ...
written 3.5 years ago by bilal.sarwar10
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Help required to Rectify/reformat the fasta header of nr database fasta sequences
... Hello all I am a beginner in bioinformatics. I have downloaded the complete nr database from the NCBI. it contains106785170 nr protein sequences altogether. the fasta header of every sequence start with fatsta symbol > followed by the accession number and other information. here is the examples ...
fasta ncbi header rna-seq blast written 3.5 years ago by bilal.sarwar10 • updated 3.5 years ago by Pierre Lindenbaum130k
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(Closed) xml extension is missing in blastx generated files. how to add it
... Hello all I have multiple subsets of blastx generated files, but all these files are without XML extension format. someone suggested me this command to rename them all in one go. rename 's/(.*)/$1.xml/ * this one is not working in my case. please help to sort out this issue. It urgent. tha ...
xml rna-seq blast annotation written 3.7 years ago by bilal.sarwar10
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How to determine number of unigenes from conigs (De Novo Assembly developed Trinity)
... Hello all i am new in field of genomics. recently i assembled my paired end RNA-seq data by trinity de novo assembler. Statistic asalysis showed that it produced 98343 contigs with the average mean length 875. Now i am confused either these are the unigenes too or i have to calculate by some other ...
gene assembly contigs rna-seq unigene written 3.8 years ago by bilal.sarwar10
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(Closed) How to download the Sequences in Fasta format from the green plant Taxonomy ID txid33090
... Hello all I am working on the denovo assembly non-model plant species. for Annotation purpose I am in need to download all protein sequences from the green plant taxonomy ID txid33090 https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=33090. is there any way to download all the sequences in ...
annotation rna-seq blast sequencing written 3.8 years ago by bilal.sarwar10
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Trinity.fasta file missing "does not exist in the out directory:
... Hello i ran the Trinity for denovo assembly on paired-end RNA-Seq data. it completed successfully after 52h of processing. but the trinity.fasta file is missing in the out folder directory. here is the code that i used /home/bilal/RNA_Seq_Project/trinityrnaseq-2.2.0/Trinity --seqType fq \ ...
software error assembly next-gen rna-seq written 4.1 years ago by bilal.sarwar10 • updated 5 days ago by eozcan10
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Comment: C: problem in Abundance Estimation using RSEM
... Thanks a lot @WouterdeCoster for your valuable suggestion. it's fixed NOW :) GOD bless you thanks ...
written 4.1 years ago by bilal.sarwar10
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Comment: C: problem in Abundance Estimation using RSEM
... thanks for your response @WouterDeCoster ##fixed now above mentioned ---------- when i run the **align_and_estimate_abundance.pl** with the command /home/bilal/Denovo/trinityrnaseq-2.2.0/util/align_and_estimate_abundance.pl --seqType fq \ --transcripts /home/bilal/Denovo/test/trinity_AssebleSe ...
written 4.1 years ago by bilal.sarwar10

Latest awards to bilal.sarwar

Popular Question 2.1 years ago, created a question with more than 1,000 views. For How to determine number of unigenes from conigs (De Novo Assembly developed Trinity)
Popular Question 3.5 years ago, created a question with more than 1,000 views. For problem in Abundance Estimation using RSEM

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