User: luigi.marongiu

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Posts by luigi.marongiu

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Use of Deconseq chromosome libraries
... Dear all, I created a database with the human sequences using the following command: bwa64 index -p hs_ref_GRCh38_p2 -a bwtsw hs_ref_GRCh38_p2_split_PS.fa.fasta > bwa.log 2 >&1   This created a series of files that I placed in a subfolder named refChr. The list of files is:   hs_r ...
myposts deconseq human contaminants written 3.9 years ago by luigi.marongiu0 • updated 12 months ago by Biostar ♦♦ 20
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Comment: C: Deconseq to remove human sequences
... I created the database with the human sequences using: bwa64 index -p hs_ref_GRCh38_p2 -a bwtsw hs_ref_GRCh38_p2_split_PS.fa.fasta > bwa.log 2 >&1 This as created a series of files that I placed in a subfolder named refChr. The list of files is: hs_ref_GRCh38_p2.amb hs_ref_GRCh38_p2.pac ...
written 3.9 years ago by luigi.marongiu0
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Comment: C: run Trinity on a server
... Thanks for the answer. Actually you are spotting some of the troubles I got with the command. I use SpiderOak because it is a shared folder that I can access at home and at work; it behaves as a normal folder on the PC so as long as I have hard drive space, there should not be a problem, I clean up ...
written 4.0 years ago by luigi.marongiu0
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run Trinity on a server
... Hello, I ran Trinity with this command sudo Trinity --seqType fq --max_memory 10G --no_bowtie --no_version_check --left pairedA_c20lr1,pairedB_c20lr1 --right unpairedA_c20lr1,unpairedB_c20lr1 --CPU 10 but i got the present error: * Running CMD: /usr/local/lib/Trinity/Inchworm/bin//inchworm -- ...
de novo assembly trinity inchworm written 4.0 years ago by luigi.marongiu0 • updated 2.6 years ago by Biostar ♦♦ 20
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Comment: C: Trinity assembly from Trimmomatic output
... I knew about (1), but then how can I use the parameters to run it? and I had the trimmed data already. For (2) it worked, but then I got a memory error message; for (3) how shall I feed the files to Trinity? -- left pairedA,pairedB --right unpairedA,unpairedB? Or simply --left pairedA --right paired ...
written 4.0 years ago by luigi.marongiu0
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Trinity assembly from Trimmomatic output
... Hello, I am running Trinity from paired sequences which have been trimmed from low quality and adaptors using Trimmomatic. The output of Trimmomatic is formed by 4 files -- two paired and two unpaired -- and I understand Trinity can get multiple files as comma separated. Here are the commands I wro ...
de novo assembly trinity written 4.0 years ago by luigi.marongiu0 • updated 4.0 years ago by h.mon28k
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Comment: C: Trinity command for paired sequences (Illumina)
... Thanks. For 2 and 3, I applied them and now it is going fine; but for 1, since the current version of bowtie is bowtie2, how can I run Trinity with the latest bowtie? Or it is necessary to use bowtie for a de novo assembly? ...
written 4.0 years ago by luigi.marongiu0
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Trinity command for paired sequences (Illumina)
... Dear all, I ran Trinity to create a de novo alignment of two paired files <myFile_1.fq> and <myFile_2.fq>, with the following: Trinity --seqType fq --max_memory 10G --no_bowtie --left /path/myFile_1.fq --right /path/myFile_2.fq --CPU 10 but i got the error: $ Trinity version: v2.1. ...
trinity de novo alignment written 4.0 years ago by luigi.marongiu0 • updated 4.0 years ago by h.mon28k
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Comment: C: Deconseq to remove human sequences
... Thank you very much, but it still a bit beyond me. So first of all, if I have two paired files, why there is only one in the command? Secondly, what configuration file shall I modify? Thirdly, the database location should go in the same config file? Should these modification be done verbatim? Cheers ...
written 4.0 years ago by luigi.marongiu0
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Deconseq to remove human sequences
... Hello, I am using Deconseq to remove human sequences from fastq files generated by Myseq Illumina. I created the database with the human sequences using: bwa64 index -p hs_ref_GRCh38_p2 -a bwtsw hs_ref_GRCh38_p2_split_PS.fa.fasta > bwa.log 2 >&1 but now I don't know how to remove these ...
cleaning deconseq written 4.0 years ago by luigi.marongiu0 • updated 4.0 years ago by satshil.r50

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