User: Ric

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Ric290
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Posts by Ric

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Failed to merge BAM files
... Hi, I have the following bash script: #!/bin/bash #usage: sh split_bam2sam-fasta_pbs.sh /path/to/reference.fasta /path/to/outputfolder/ /path/to/input/*.sorted.dedup.bam output=$2 mkdir $output merged=$(basename ${output}) echo $merged #samlist=$(printf 'I="%s" ' "$ ...
samtools bash written 2 hours ago by Ric290 • updated 2 hours ago by Shalu Jhanwar60
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orthomcl to venn diagram
... Hi, I found [orthomclToVenn][1] which allows to create venn diagramms from orthomcl results. Unfortunately, I do not know how to create the `families.txt` (this file details which species are in which groups, first the name of the group, then the short handles that appear in groups.txt). Example: ...
family genes ortholog venn diagram orthomcl written 20 days ago by Ric290
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Comment: C: Create de novo repeat library
... Are the below steps correct? > wget -c https://www.dfam.org/releases/Dfam_3.1/families/Dfam.embl.gz > gunzip Dfam.embl.gz > mv Dfam.embl ${CONDA_PREFIX}/share/RepeatMasker/Libraries/ > cd ${CONDA_PREFIX}/share/RepeatMasker/Libraries/ > ../util/buildRMLibFromEMBL. ...
written 11 weeks ago by Ric290
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Comment: C: StringTie output to train Augustus
... Thank you, is there a way or necessary to add strand information to the output of bam2hints? **UPDATE:** Bam2hints resutls: > wc -l .intron-hints.gff 438503 .intron-hints.gff . > head .intron-hints.gff NbV1Ch01 b2h intron 212732 212828 0 . . ...
written 3 months ago by Ric290
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StringTie required filtered BAM
... Hi, AUGUSTUS comes with a script which can filter BAM files filterBam –uniq –paired –pairwiseAlignment –in Aligned.out.ss.bam –out Aligned.out.ssf.bam Does StringTie does any filtering by its own or would it be possible to improve StringTie by using the above script? Thank you in advance ...
gene annotation rna-seq assembly written 3 months ago by Ric290 • updated 3 months ago by kristoffer.vittingseerup3.3k
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Comment: C: StringTie output to train Augustus
... Thank you for your link. I also found [Incorporating RNA-Seq into AUGUSTUS](http://augustus.gobics.de/binaries/readme.rnaseq.html) but they used BLAT. However, I have done all my alignment with HIsat2. Does anyone know how to change the commands to BAM files? ...
written 3 months ago by Ric290
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StringTie output to train Augustus
... Hi, I ran StringTie and transdecoder. How is it possible to use these outputs as input for Augustus to predict genes with UTR? Thank you in advance ...
gene annotation written 3 months ago by Ric290
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Comment: C: Create de novo repeat library
... Thank you. I did: > wget -c https://www.dfam.org/releases/Dfam_3.1/families/Dfam.hmm.gz > cp Dfam.hmm ${CONDA_PREFIX}/share/RepeatMasker/Libraries Where, can I find a free RepBase alternative for academics? Or can I anyhow create it from Dfam? Thank you in advance, ...
written 3 months ago by Ric290
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Comment: C: Create de novo repeat library
... I ran `RepeatModeler -engine ncbi -database Repeats -pa 8` but I can not find `consensi.fa.classified`. Furthermore, the output folder contain the following files: ls RM_56831.ThuMar191408352020/ consensi.fa families.stk round-1 round-2 round-3 round-4 round-5 round-6 tmpBlastXResul ...
written 3 months ago by Ric290
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Comment: C: Repeats detection in a genome
... Yes, I would like to detect (de-novo) repeats in your genome. Therefore, I changed my question above. ...
written 4 months ago by Ric290

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