I have generated fastq files (R1& R2) from the mapped bam file and I am now interested in assembling those reads using velvet. I need guidance to how to run velveth, velvetg and viewing the output.
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Originally posted by Michael.Ante View PostHi Kaps,
you should have a look at the Bowtie2 homepage. There, it is explained in detail how the programs work. At the end of the manual is a "Lambda phage example", which has quite an overlap to your problem. It also has a SAMtools downstream section...
Cheers,
Michael
here is the feedback: samtools view -bS 4_S4_paired.sam 4_S4_paired.bam
[main_samview] random alignment retrieval only works for indexed BAM or CRAM files.
▒BC▒m▒▒N▒0D▒ܜK▒X=p[▒qU|
▒ ▒▒▒5r[SY▒I▒▒▒O▒sH[@▒▒▒f▒▒▒a0▒w3▒Rʄq▒▒G▒[▒2▒▒Q▒Lk▒▒ vU▒1)J▒ei▒M&"▒qq5▒Q^ݒ▒▒▒▒▒`▒ U▒▒▒Q▒ vI▒▒▒f▒▒q▒▒:;▒=▒▒P▒▒U▒▒"n\o3▒ε▒
▒;*(n▒J)*▒▒▒▒֙%▒zM19H▒I▒▒▒▒▒5{▒>▒S▒H▒Qt▒~▒▒▒
▒▒y▒▒
when with -bT, I get a similar feedback as;
samtools view -bT cp4genome.fa 4_S4_paired.sam 4_S4_paired.bam
[samfaipath] build FASTA index...
[fai_build_core] different line length in sequence '4_S4_contig_23'.
[samfaipath] fail to build FASTA index.
[main_samview] random alignment retrieval only works for indexed BAM or CRAM files.
▒BC▒m▒▒N▒0D▒ܜK▒X=p[▒qU|
▒ ▒▒▒5r[SY▒I▒▒▒O▒sH[@▒▒▒f▒▒▒a0▒w3▒Rʄq▒▒G▒[▒2▒▒Q▒Lk▒▒ vU▒1)J▒ei▒M&"▒qq5▒Q^ݒ▒▒▒▒▒`▒ U▒▒▒Q▒ vI▒▒▒f▒▒q▒▒:;▒=▒▒P▒▒U▒▒"n\o3▒ε▒
▒;*(n▒J)*▒▒▒▒֙%▒zM19H▒I▒▒▒▒▒5{▒>▒S▒H▒Qt▒~▒▒▒
where is the problem?
Comment
-
Hi Kaps,
tryCode:samtools view -S 4_S4_paired.sam | head
Code:samtools view -bSh 4_S4_paired.sam > 4_S4_paired.bam
Cheers,
Michael
Comment
Latest Articles
Collapse
-
by seqadmin
While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...-
Channel: Articles
Today, 07:15 AM -
-
by seqadmin
Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.
Somatic Genomics
“We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...-
Channel: Articles
05-24-2024, 01:16 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Today, 08:18 AM
|
0 responses
10 views
0 likes
|
Last Post
by seqadmin
Today, 08:18 AM
|
||
Started by seqadmin, Today, 08:04 AM
|
0 responses
12 views
0 likes
|
Last Post
by seqadmin
Today, 08:04 AM
|
||
Started by seqadmin, 06-03-2024, 06:55 AM
|
0 responses
13 views
0 likes
|
Last Post
by seqadmin
06-03-2024, 06:55 AM
|
||
Started by seqadmin, 05-30-2024, 03:16 PM
|
0 responses
27 views
0 likes
|
Last Post
by seqadmin
05-30-2024, 03:16 PM
|
Comment