User: shuksi1984
shuksi1984 • 20
- Reputation:
- 20
- Status:
- New User
- Location:
- Last seen:
- 1 day, 5 hours ago
- Joined:
- 2 months, 2 weeks ago
- Email:
- s*********@gmail.com
Posts by shuksi1984
<prev
• 68 results •
page 1 of 7 •
next >
0
votes
2
answers
83
views
2
answers
Comment:
C: GATK3 error message
... I ran the above command and got same output. I could not find any file in my working directory, except the output as shown above. I am unable to understand. Kindly, explain ...
written 2 days ago by
shuksi1984 • 20
0
votes
2
answers
83
views
2
answers
Comment:
C: GATK3 error message
... your data is corrupted
bam file is corrupted?
...
written 3 days ago by
shuksi1984 • 20
0
votes
2
answers
83
views
2
answers
Comment:
C: GATK3 error message
... Can you share the link to download hg38gatkbundle reference genome? I am trying with the given link:
ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/Homo_sapiens_assembly38.fasta.gz ...
written 3 days ago by
shuksi1984 • 20
0
votes
2
answers
83
views
2
answers
Comment:
C: GATK3 error message
... > what is the version of gatk ?
GATK3.8
Output of
grep -v '^>' /path/to/Homo_sapiens_assembly38.fasta | tr -d '[ATGCNatgcn\n]' | grep -o '.' | sort | uniq -c
is:
2 \
2 B
1 F
1 I
15 K
8 M
2 O
26 R
4 S
13 W
33 Y ...
written 3 days ago by
shuksi1984 • 20
0
votes
2
answers
83
views
2
answers
... I ran following command:
java -Xmx4g -jar /path/to/gatk3.8.jar -T RealignerTargetCreator -R /path/to/Homo_sapiens_assembly38.fasta -I SP1_markduplicate.bam -o SP1_realignedtargets.list
I got following error message:
ERROR MESSAGE: Bad input: We encountered a non-standard non-IUPAC base in ...
written 3 days ago by
shuksi1984 • 20
• updated
3 days ago by
Devon Ryan ♦ 81k
0
votes
0
answers
81
views
0
answers
... bwa-Version: 0.7.12-r1039
OS-Ubuntu 16.04.3 LTS (xenial)
> In the command you gave above I cannot see why this happens
It is because I used, nohup? ...
written 4 days ago by
shuksi1984 • 20
0
votes
0
answers
81
views
0
answers
... The command
grep -m 10 -v "^@" SRR6876052_mem.sam
Gives following output:
[M::bwa_idx_load_from_disk] read 3171 ALT contigs
[M::process] read 66226 sequences (10000126 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 27774, 2, 0)
[M::mem_pestat] skip ...
written 4 days ago by
shuksi1984 • 20
0
votes
0
answers
81
views
0
answers
... > Beside this we need the first few lines that doesn't start by @
how do we achieve that? Is my file corrupt? ...
written 4 days ago by
shuksi1984 • 20
0
votes
0
answers
81
views
0
answers
...
Following are the 1st few lines of sam file
>@SQ SN:chr1 LN:248956422
> @SQ SN:chr2 LN:242193529
>@SQ SN:chr3 LN:198295559
> @SQ SN:chr4 LN:190214555
> @SQ SN:chr5 LN:181538259
> @SQ SN:chr6 LN:170805979
>@SQ SN:chr7 LN:159345973
>@SQ SN:chr8 LN:145138636
>@SQ ...
written 4 days ago by
shuksi1984 • 20
1
vote
0
answers
81
views
0
answers
... What does SAMFormatException mean? How to troubleshoot this error. I got following error:
> Exception in thread "main" htsjdk.samtools.SAMFormatException: Error
> parsing text SAM file. Not enough fields; File SRR6876052_mem.sam;
> Line 1
My command is:
nohup java -jar path/to/pi ...
written 4 days ago by
shuksi1984 • 20
Latest awards to shuksi1984
Rising Star
12 days ago,
created 50 posts within first three months of joining.
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 659 users visited in the last hour