User: marongiu.luigi

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Posts by marongiu.luigi

<prev • 59 results • page 1 of 6 • next >
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Comment: C: syntax tophat2 for reference index
... It worked. I built bowtie2 2.3.3.1 from source and this time everything went smoothly. I could even use a fixed folder where I ma keeping the reference indices (/home/RefSeq/Human): tophat2 -o SRR390728_aln --transcriptome-index=/home/RefSeq/Human/Hsapiens_GRCh38.tr/Hsapiens_GRCh38 /home/RefSe ...
written 7 days ago by marongiu.luigi90
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Comment: C: Build Bowtie2 2.3.3.1 with make on linux 64 bit
... Yes, it worked (I did not need libtbb-dev when I built the previous version). Thank you. ...
written 8 days ago by marongiu.luigi90
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Build Bowtie2 2.3.3.1 with make on linux 64 bit
... Hello, I am trying to build [bowtie 2 version 2.3.3.1][1] from source using the command make but I get the following: /bowtie2$ make g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK ...
software error written 8 days ago by marongiu.luigi90
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Comment: C: syntax tophat2 for reference index
... Thank you. I have upgraded Bowtie to 2.3.3.1 using the [precompiled version for linux 64 bit][1]; the version 2.2.9.0 I was using instead was generated from the source with make. However, while with the former version it took me overnight to generate the index, with the newer I had to stop it after ...
written 8 days ago by marongiu.luigi90
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Comment: C: syntax tophat2 for reference index
... I even tried to remove the .tr from the index name: $ tophat2 -o SRR390728_aln --transcriptome-index=./Hsapiens_GRCh38 Hsapiens_GRCh38 paired1.fq paired2.fq [2017-10-12 16:12:02] Beginning TopHat run (v2.1.1) ----------------------------------------------- [2017-10-12 16:12:02] ...
written 11 days ago by marongiu.luigi90
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Comment: C: syntax tophat2 for reference index
... The indexing looked done OK, there were no error messages. I provided the list of files in use; does not look to me there is something missing. ...
written 11 days ago by marongiu.luigi90
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Comment: C: syntax tophat2 for reference index
... I got the following: $ tophat2 -o SRR390728_aln --transcriptome-index=Hsapiens_GRCh38.tr/Hsapiens_GRCh38 paired1.fq paired2.fq [2017-10-12 16:05:10] Beginning TopHat run (v2.1.1) ----------------------------------------------- [2017-10-12 16:05:10] Checking for Bowtie B ...
written 11 days ago by marongiu.luigi90
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Comment: C: syntax tophat2 for reference index
... I know, it is nostalgia indeed. I am already switching to STAR and HISAT, but I wanted to get to know Tophat for completion. The index was built a folder above Hsapiens_GRCh38.tr (actually the latter was created by Tophat). ...
written 11 days ago by marongiu.luigi90
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syntax tophat2 for reference index
... Hello, I want to use Tophat to align reading for RNA-seq analysis. I downloaded the sequences SRR390728_1.fastq and SRR390728_2.fastq, quality trimmed with java -jar /usr/bin/trimmomatic PE SRR390728_1.fastq SRR390728_2.fastq paired1.fq unpaired_1.fq paired2.fq unpaired_2.fq SLIDINGWINDOW:4:20 ...
rna-seq written 11 days ago by marongiu.luigi90 • updated 11 days ago by e.rempel510
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Comment: C: run FASTQC on linux terminal as java script
... That was it! I downloaded the distro from [here][1], changed the mode of the perl file with **chmod 755 fastqc** and it does work perfectly. Thank you! (this [tip][2] is instead obviously wrong) [1]: http://%20https://www.bioinformatics.babraham.ac.uk/projects/download.html [2]: http://install ...
written 15 days ago by marongiu.luigi90

Latest awards to marongiu.luigi

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