User: rahmati.razieh83

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Posts by rahmati.razieh83

<prev • 23 results • page 1 of 3 • next >
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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 5 weeks ago by rahmati.razieh8310 • updated 5 weeks ago by Devon Ryan74k
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Comment: C: trimming PE RNA Reads
... Thanks a lot for your help ...
written 8 weeks ago by rahmati.razieh8310
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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 8 weeks ago by rahmati.razieh8310
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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 8 weeks ago by rahmati.razieh8310
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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 8 weeks ago by rahmati.razieh8310
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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 8 weeks ago by rahmati.razieh8310
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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 8 weeks ago by rahmati.razieh8310
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Comment: C: mapping and quantification of paired end reads using BBmap
... Dear ahmad; Thanks alot for your comment. I have already trimmed universal adapters by trimmomatic. But I found out, in addition to adapters my reads contains some random Lexogen primers. because of existing these primers, I have been recommended to use bbmap instead of top hat2 for mapping the read ...
written 8 weeks ago by rahmati.razieh8310
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Comment: C: trimming PE RNA Reads
... before assembly I trimmed adapters but not Lexogen primers. So I think this assembly contains Lexogen primers ...
written 8 weeks ago by rahmati.razieh8310
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Comment: C: trimming PE RNA Reads
... thanks a lot for your comment. According to what you recommended me, I decided to keep Lxogen primer but use bbmap instead of Tophat2 to map the reads. I assembled paired end reads with trinity and now I have a trinity.fasta file. for the next step I need to map paired end reads to de novo assembl ...
written 8 weeks ago by rahmati.razieh8310

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