User: alvarocentron91

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Posts by alvarocentron91

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Comment: C: BEDTools coverage or intersect
... I had a space at the begining of chr in one of the files. I feel stupid now hahah. Many thanks! ...
written 3 months ago by alvarocentron910
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Comment: C: BEDTools coverage or intersect
... Sorry, I should have explained better ...
written 3 months ago by alvarocentron910
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Comment: C: BEDTools coverage or intersect
... But I have used the same format before and I got results: chr22 StringTie exon 354097 359650 1000 + . gene_id "MSTRG.8010"; transcript_id "MSTRG.8010.1"; exon_number "1"; 1 475 5554 0.0855239 And the program is supposed to work with gff and gtf ...
written 3 months ago by alvarocentron910
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BEDTools coverage or intersect
... Hello, I'm having a problem with bedtools that I don't know how to solve. I have a file with this kind of information: chr19 frame_2_peak_20020 noCDS 184940 185402 . + . 433 And another one with: chr19 StrAnA transcript 184909 186112 . + . gene_id "candidate_350"; They are obviously over ...
software error written 3 months ago by alvarocentron910
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Comment: C: STAR: truncated .sam
... I used a sbatch queue with: #!/bin/bash #SBATCH -N 1 #SBATCH -n 18 #SBATCH -J star_mapping #SBATCH -p day #SBATCH -o star_mapping.out #SBATCH -e ERRORstar_mapping.err #SBATCH --constraint="SET2" #SBATCH --mem=92gb I got some warnings, but no problems with the ma ...
written 4 months ago by alvarocentron910
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Comment: C: STAR: truncated .sam
... I used the default option, anyways I finally found the problem, it was in the index. Thank you! ...
written 4 months ago by alvarocentron910
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STAR: truncated .sam
... Hello guys, I have generated a SAM file using the following line with STAR: STAR --runThreadN 18 --genomeDir /home/acenbro/Doct2.0/Genomes/Ustilago/STAR_index --readFilesIn ../ax2_1_paired.fastq ../ax2_2_paired.fastq --sjdbGTFfile /home/acenbro/Doct2.0/Genomes/Ustilago/p3_t237631_Ust_maydi_v2GB ...
rna-seq written 4 months ago by alvarocentron910
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Comment: C: STAR index doesn't finish
... There are no log.error files generated, and in the subsection "Log files" from STAR's manual there are no indications on how to generate them, just the log.out and the log.progress.out (which has not been generated). I'm running the command directly in a Slurm job allocation. The thing is that 1 ...
written 5 months ago by alvarocentron910
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Comment: C: STAR index doesn't finish
... I'm not sure how to do that, however, I re-ran the program increasing the RAM up to 90GB and now the message: > EXITING because of fatal ERROR: could noSep 19 12:48:03 doesn't show anymore. There is only one warning message: WARNING: long repeat for junction # 1350 : Um_chr06 1022586 10233 ...
written 5 months ago by alvarocentron910
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STAR index doesn't finish
... Hello, I'm having some problems indexing my genome with STAR, I have used the following line code: STAR --runThreadN 5 --runMode genomeGenerate --genomeDir STAR_index --genomeFastaFiles p3_t237631_Ust_maydi_v2GB.scaf.fa --sjdbGTFfile p3_t237631_Ust_maydi_v2GB.gtf --sjdbOverhang 88 --limitGenom ...
star rna-seq written 5 months ago by alvarocentron910

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