User: rahmati.razieh83

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Posts by rahmati.razieh83

<prev • 26 results • page 1 of 3 • next >
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Comment: C: selection soft Power in WGCNA
... Dear Andres Thanks for your answer I am new in WGCNA, so I do not how to perform WGCNA on my data. But as you answer to my question, I reduced the number of contigs I got from RNA Seq. I had a transcriptome data with 303000 contigs and after removing the redundant transcripts by Cd-Hit_EST and filt ...
written 9 months ago by rahmati.razieh8330
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selection soft Power in WGCNA
... Hi everyone I'm running WGCNA pipeline for 18 samples with about 60000 genes. I do not know which soft power I should consider regarding the plots. As scale independence plot shows two section I do not know whether 4 or 19 should be considered as soft power. Please guide me. ![enter image descripti ...
rna-seq written 9 months ago by rahmati.razieh8330 • updated 8 months ago by tujuchuanli60
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Is there any alternative for CD_Hit to remove redundancy from asemmbled trinity output file?
... Hi everyone I have a problem with reduction of redundancy from trinity output file. I have got an assembled fasta file from trinity containing 302000 contigs showing so much redundancy. I used CD_hit to remove redundancies and get unigenes. After using CD_Hit the number of contigs reduced to 24000 ...
assembly written 23 months ago by rahmati.razieh8330 • updated 23 months ago by Jake Warner810
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kallisto K-mer size
... Dear every one I have a fasta denovo assembled file provided by trinity with the kmer size=25. I want to make quantification by Kallisto but the kmer size of kallisto is 31by defaulte. Is it necessary to change the K-mer size of kallisto to 25 or I can use kallisto with the kmer size=31? If it is ...
alignment written 2.5 years ago by rahmati.razieh8330 • updated 2.3 years ago by Biostar ♦♦ 20
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Comment: C: trimming PE RNA Reads
... Thanks a lot for your help ...
written 2.5 years ago by rahmati.razieh8330
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Comment: C: trimming PE RNA Reads
... Many thanks for the command. these commands are for removal of specific number of nucleotides from the end of the read? Is there any other command to remove specific number of nucleotides from the start of the read as I need to remove 9 nucleotide from the 5' side of R1? ...
written 2.5 years ago by rahmati.razieh8330
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Comment: C: trimming PE RNA Reads
... I do not know how trinity can solve the problem of primers. So regarding the comments maybe it is better to remove primers from the reads. My question is that which software is more efficient for primer removal? according to Lexogen protocol I must remove 9 nucleotides from 5' side of R1 and 6 nuc ...
written 2.5 years ago by rahmati.razieh8330
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Comment: C: Extract sequence from fasta using primer
... Dear Brian I received some paired end reads containing 9 nucleotides in 5’ of Read1 as stater and 6 nucleotides in 3’ side of read2 as stopper random primers. So I need to remove 9 nucleotides from 5’ of Read1 and 6 nucleotides from 3’ side of read2. How can I remove these random primers by using B ...
written 2.5 years ago by rahmati.razieh8330
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Comment: C: trimming PE RNA Reads
... According to what Michael has suggested I can keep the primers. What is your suggestion? ...
written 2.5 years ago by rahmati.razieh8330
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Comment: C: Calculate FPKM value from bam files
... dear Brian can we get FPKM directly d for paired end reads from bbmap or bbmap just give us RPKM? ...
written 2.5 years ago by rahmati.razieh8330

Latest awards to rahmati.razieh83

Popular Question 9 months ago, created a question with more than 1,000 views. For kallisto K-mer size
Popular Question 9 months ago, created a question with more than 1,000 views. For kallisto K-mer size
Popular Question 20 months ago, created a question with more than 1,000 views. For trimming PE RNA Reads

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