User: m.t.lorenc
m.t.lorenc • 0
- Reputation:
- 0
- Status:
- New User
- Last seen:
- 3 months, 2 weeks ago
- Joined:
- 7 years, 7 months ago
- Email:
- m*********@gmail.com
Profile information, website and location are not shown for new users.
This helps us discourage the inappropriate use of our site.
Posts by m.t.lorenc
<prev
• 11 results •
page 1 of 2 •
next >
0
votes
0
answers
1.6k
views
0
answers
... Did you find the problem? ...
written 15 months ago by
m.t.lorenc • 0
0
votes
3
answers
16k
views
3
answers
... Could you please provide an example? ...
written 19 months ago by
m.t.lorenc • 0
0
votes
3
answers
16k
views
3
answers
... 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 19 months ago by
m.t.lorenc • 0
3
votes
1
answer
750
views
1
answer
... 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 ...
written 20 months ago by
m.t.lorenc • 0
• updated
19 months ago by
ATpoint ♦ 44k
0
votes
1
answer
1.3k
views
1
answers
... Thank you, do you think `java -jar picard.jar SortSam I=input.sam O=sorted.samSORT_ORDER=coordinat` would be slower? ...
written 21 months ago by
m.t.lorenc • 0
0
votes
1
answer
1.3k
views
1
answer
... 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,
...
written 21 months ago by
m.t.lorenc • 0
0
votes
1
answer
1.8k
views
1
answers
... 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 21 months ago by
m.t.lorenc • 0
0
votes
1
answer
4.8k
views
1
answers
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 22 months ago by
m.t.lorenc • 0
1
vote
1
answer
4.8k
views
1
answer
... 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 ...
written 22 months ago by
m.t.lorenc • 0
• updated
22 months ago by
jflopezfernandez • 40
1
vote
0
answers
326
views
0
answers
... 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?
...
written 22 months ago by
m.t.lorenc • 0
Latest awards to m.t.lorenc
Popular Question
16 months ago,
created a question with more than 1,000 views.
For Definition Of Genome And Snp Annotation
Popular Question
3.1 years ago,
created a question with more than 1,000 views.
For Definition Of Genome And Snp Annotation
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 964 users visited in the last hour