User: m.t.lorenc

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m.t.lorenc0
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Posts by m.t.lorenc

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Eukaryotic gene annotation transfer tools
... Did you find the problem? ...
written 12 months ago by m.t.lorenc0
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Comment: C: How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
... Could you please provide an example? ...
written 16 months ago by m.t.lorenc0
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Answer: A: How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
... Hi, I ran `hisat2 -p 8 -x ${2%.*} -1 $r1 -2 $r2 | grep -v "XS:i:" | samtools view -@ 8 -h -F 2316 -f 0x2 - | samtools fixmate - - | samtools sort -@ 8 - -o ${3}/${output}.sorted.bam`. As result I got: 12681015 reads; of these: 12681015 (100.00%) were paired; of these: 1600731 (12. ...
written 16 months ago by m.t.lorenc0
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SRA to FASTQ problem
... Hi, I downloaded RNA-Seq data from NCBI and used `fastq-dump --gzip --skip-technical --readids --read-filter pass --dumpbase --split-3 --clip SRR1043177.sra` to convert into FASTQ. However, it appears that header in `@` and `+` are different: > zcat SRR1043177_pass_1.fastq.gz | head @HW ...
next-gen rna-seq sequencing written 17 months ago by m.t.lorenc0 • updated 17 months ago by ATpoint40k
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Comment: C: samtools sort: truncated file. Aborting
... Thank you, do you think `java -jar picard.jar SortSam I=input.sam O=sorted.samSORT_ORDER=coordinat` would be slower? ...
written 18 months ago by m.t.lorenc0
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samtools sort: truncated file. Aborting
... Hi, I got an error by using this the below command: samtools sort -O SAM -n -@ 2 -o OZBenth2_.fastp.fq.gz.name-sorted.sam OZBenth2_.fastp.fq.gz.sam [W::sam_read1] Parse error at line 1 samtools sort: truncated file. Aborting What did I miss? Thank you in advance, ...
alignment picard samtools written 18 months ago by m.t.lorenc0
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Comment: C: How to create/get cytoband file for Maize (non-model organism) genome
... I found [here](http://software.broadinstitute.org/software/igv/cytoband) is a description of the file format. I can write a script which gets the first 3 columns values out `samtools faidx` output. Does anyone know how to determine the last 2 columns (name and gieStain)? ...
written 19 months ago by m.t.lorenc0
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Comment: C: hisat2-align exited with value 1
... Thank you all for your response, but I still get the same problem: > hisat2 -p 12 --rg-id JoshP-S9-RI37_S5_L004__001.fastq.gz --rg JoshP-S9-RI37_S5_L004__001.fastq.gz --rg JoshP-S9-RI37_S5_L004__001.fastq.gz --rg JoshP-S9-RI37_S5_L004__001.fastq.gz --rg JoshP-S9-RI37_S5_L004__001.fastq.gz -- ...
written 19 months ago by m.t.lorenc0
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hisat2-align exited with value 1
... Hi, I have got the following error samblaster: Version 0.1.24 samblaster: Inputting from stdin samblaster: Outputting to stdout Error reading _rstarts[] array: 16256, 20484 Error: Encountered internal HISAT2 exception (#1) Command: /work/waterhouse_team/miniconda2/envs/hisa ...
alignment rna-seq written 19 months ago by m.t.lorenc0 • updated 19 months ago by jflopezfernandez40
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Hisat2 index creating
... I tried to run hisat2_extract_splice_sites.py genes.gtf > genes.ss hisat2_extract_exons.py genes.gtf > genes.exon Unfortunately, both files are empty. What did I miss? ...
alignment rna-seq written 20 months ago by m.t.lorenc0

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Popular Question 14 months ago, created a question with more than 1,000 views. For Definition Of Genome And Snp Annotation
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Definition Of Genome And Snp Annotation

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