User: rahmati.razieh83

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Posts by rahmati.razieh83

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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 4 months ago by rahmati.razieh8320 • updated 4 months ago by Jake Warner670
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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 11 months ago by rahmati.razieh8320 • updated 9 months ago by Biostar ♦♦ 20
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Comment: C: trimming PE RNA Reads
... Thanks a lot for your help ...
written 11 months ago by rahmati.razieh8320
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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 11 months ago by rahmati.razieh8320
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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 11 months ago by rahmati.razieh8320
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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 11 months ago by rahmati.razieh8320
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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 11 months ago by rahmati.razieh8320
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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 11 months ago by rahmati.razieh8320
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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 11 months ago by rahmati.razieh8320
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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 11 months ago by rahmati.razieh8320

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